ClinVar Genomic variation as it relates to human health
NM_007294.4(BRCA1):c.3018_3021del (p.His1006fs)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_007294.4(BRCA1):c.3018_3021del (p.His1006fs)
Variation ID: 54749 Accession: VCV000054749.32
- Type and length
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Deletion, 4 bp
- Location
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Cytogenetic: 17q21.31 17: 43092510-43092513 (GRCh38) [ NCBI UCSC ] 17: 41244527-41244530 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 1, 2014 Oct 20, 2024 Sep 8, 2016 - HGVS
- ... more HGVS ... less HGVS
- Protein change
- H959fs, H1006fs, H710fs, H838fs, H936fs, H958fs, H965fs, H1005fs, H1003fs, H878fs, H879fs, H895fs, H918fs, H935fs, H939fs, H980fs, H894fs, H917fs, H938fs, H964fs, H979fs
- Other names
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3137del4
3137delTTCA
3135del4
- Canonical SPDI
- NC_000017.11:43092509:TGAATG:TG
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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BRCA1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
13041 | 14847 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (11) |
reviewed by expert panel
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Sep 8, 2016 | RCV000111982.26 | |
Pathogenic (2) |
criteria provided, single submitter
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Jan 27, 2024 | RCV000496722.14 | |
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Mar 23, 2023 | RCV000581897.16 | |
Pathogenic (1) |
no assertion criteria provided
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Dec 1, 2018 | RCV000785405.10 | |
Pathogenic (1) |
no assertion criteria provided
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Jun 11, 2019 | RCV001271011.9 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Jun 1, 2024 | RCV003133127.13 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Sep 08, 2016)
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reviewed by expert panel
Method: curation
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Breast-ovarian cancer, familial, susceptibility to, 1
Affected status: unknown
Allele origin:
germline
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Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)
Accession: SCV000299874.2
First in ClinVar: Sep 24, 2016 Last updated: Sep 24, 2016 |
Comment:
Variant allele predicted to encode a truncated non-functional protein.
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Pathogenic
(Nov 03, 2014)
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criteria provided, single submitter
Method: clinical testing
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Breast-ovarian cancer, familial, susceptibility to, 1
Affected status: yes
Allele origin:
germline
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Michigan Medical Genetics Laboratories, University of Michigan
Accession: SCV000195913.1
First in ClinVar: Mar 29, 2015 Last updated: Mar 29, 2015 |
Tissue: Blood
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Pathogenic
(Dec 30, 2020)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Color Diagnostics, LLC DBA Color Health
Accession: SCV000688412.2
First in ClinVar: Feb 19, 2018 Last updated: Jun 19, 2021 |
Comment:
This variant deletes 4 nucleotides in exon 10 of the BRCA1 gene, creating a frameshift and premature translation stop signal. This variant is expected to … (more)
This variant deletes 4 nucleotides in exon 10 of the BRCA1 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. To our knowledge, functional studies have not been reported for this variant. This variant has been observed in multiple individuals and families affected with breast and ovarian cancer (PMID: 9663595, 22923021, 26014432, 28715532, 28740454, 29907814; BIC and UMD databases). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of BRCA1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. (less)
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Pathogenic
(Sep 19, 2015)
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criteria provided, single submitter
Method: clinical testing
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Breast-ovarian cancer, familial, susceptibility to, 1
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000296391.2
First in ClinVar: Mar 29, 2015 Last updated: Jan 03, 2022 |
Indication for testing: Hereditary breast and ovarian cancer syndrome (HBOC)
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Pathogenic
(Sep 23, 2021)
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criteria provided, single submitter
Method: curation
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Sema4, Sema4
Accession: SCV002538172.1
First in ClinVar: Jun 24, 2022 Last updated: Jun 24, 2022
Comment:
The BRCA1 c.3018_3021delTTCA (p.H1006QfsX17) variant has been reported in several individuals with breast and/or ovarian cancer (PMID: 29907814, 28740454, 28715532, 26014432). This variant causes a … (more)
The BRCA1 c.3018_3021delTTCA (p.H1006QfsX17) variant has been reported in several individuals with breast and/or ovarian cancer (PMID: 29907814, 28740454, 28715532, 26014432). This variant causes a frameshift at amino acid 1006 that results in premature termination 17 amino acids downstream. At this location, this is predicted to cause nonsense-mediated decay and result in an absent protein (loss of function). Loss of function variants in BRCA1 are known to be pathogenic (PMID: 29446198). This variant is not reported in the population database Genome Aggregation Database (http://gnomad.broadinstitute.org, PMID: 32461654). This variant has been reported in ClinVar (Variation ID: 54749). Based on the current evidence available, this variant is interpreted as pathogenic. (less)
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Pathogenic
(Oct 02, 2015)
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criteria provided, single submitter
Method: clinical testing
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Breast-ovarian cancer, familial, susceptibility to, 1
Affected status: unknown
Allele origin:
germline
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Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge
Accession: SCV000325528.4
First in ClinVar: Nov 05, 2016 Last updated: Dec 11, 2022 |
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Pathogenic
(Nov 04, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV003818093.2
First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024 |
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Pathogenic
(Mar 23, 2023)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV001179248.5
First in ClinVar: Mar 16, 2020 Last updated: May 01, 2024 |
Comment:
The c.3018_3021delTTCA pathogenic mutation, located in coding exon 9 of the BRCA1 gene, results from a deletion of 4 nucleotides at nucleotide positions 3018 to … (more)
The c.3018_3021delTTCA pathogenic mutation, located in coding exon 9 of the BRCA1 gene, results from a deletion of 4 nucleotides at nucleotide positions 3018 to 3021, causing a translational frameshift with a predicted alternate stop codon (p.H1006Qfs*17). This mutation has been reported in multiple families affected with hereditary breast and/or ovarian cancer, including those of Austrian and Slovenian ancestry (Wagner TM et al. Int. J. Cancer 1998 Jul;77(3):354-60; Stegel V et al, BMC Med. Genet. 2011 Jan;12:9; Novakovi S et al. Int. J. Oncol. 2012 Nov;41(5):1619-27). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. (less)
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Pathogenic
(Mar 03, 2024)
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criteria provided, single submitter
Method: clinical testing
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Breast-ovarian cancer, familial, susceptibility to, 1
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV005058239.1
First in ClinVar: Jun 17, 2024 Last updated: Jun 17, 2024 |
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Pathogenic
(Aug 19, 2019)
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criteria provided, single submitter
Method: clinical testing
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Familial breast-ovarian cancer 1
Affected status: unknown
Allele origin:
germline
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Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine
Accession: SCV001434968.1
First in ClinVar: Oct 03, 2020 Last updated: Oct 03, 2020 |
Comment:
The c.3018_3021delTTCA (p.His1006GlnfsTer17) variant in the BRCA1 gene is predicted to introduce a premature translation termination codon. This variant is not observed in gnomAD and … (more)
The c.3018_3021delTTCA (p.His1006GlnfsTer17) variant in the BRCA1 gene is predicted to introduce a premature translation termination codon. This variant is not observed in gnomAD and is considered pathogenic by the ENIGMA expert panel (Accession: SCV000299874.2). It has been identified in three Slovene hereditary breast and ovarian cancer families (PMID 22923021). Therefore, the c.3018_3021delTTCA (p.His1006GlnfsTer17) variant in the BRCA1 gene is classified as pathogenic. (less)
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Pathogenic
(Apr 02, 2020)
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criteria provided, single submitter
Method: clinical testing
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Breast-ovarian cancer, familial, susceptibility to, 1
Affected status: yes
Allele origin:
germline
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Department of Molecular Diagnostics, Institute of Oncology Ljubljana
Accession: SCV001499615.1
First in ClinVar: Mar 07, 2021 Last updated: Mar 07, 2021 |
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Pathogenic
(Dec 09, 2022)
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criteria provided, single submitter
Method: research
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Breast-ovarian cancer, familial, susceptibility to, 1
Affected status: no
Allele origin:
germline
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Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV002762797.2
First in ClinVar: Dec 17, 2022 Last updated: Feb 25, 2023 |
Comment:
PVS1, PS4_STR PM2_SUP
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Pathogenic
(Jan 27, 2024)
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criteria provided, single submitter
Method: clinical testing
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Hereditary breast ovarian cancer syndrome
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001590197.4
First in ClinVar: May 10, 2021 Last updated: Feb 14, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.His1006Glnfs*17) in the BRCA1 gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.His1006Glnfs*17) in the BRCA1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BRCA1 are known to be pathogenic (PMID: 20104584). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with clinical features of hereditary breast and ovarian cancer syndrome (PMID: 9663595, 29907814). This variant is also known as 3135del4. ClinVar contains an entry for this variant (Variation ID: 54749). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Jun 01, 2024)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV005092696.3
First in ClinVar: Aug 04, 2024 Last updated: Oct 20, 2024 |
Comment:
BRCA1: PVS1, PM2, PS4:Moderate
Number of individuals with the variant: 1
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Pathogenic
(Feb 20, 2004)
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no assertion criteria provided
Method: clinical testing
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Breast-ovarian cancer, familial 1
Affected status: yes
Allele origin:
germline
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Breast Cancer Information Core (BIC) (BRCA1)
Accession: SCV000144610.1
First in ClinVar: Apr 01, 2014 Last updated: Apr 01, 2014 |
Observation 1:
Number of individuals with the variant: 5
Geographic origin: Austria
Observation 2:
Number of individuals with the variant: 1
Ethnicity/Population group: Western European
Observation 3:
Number of individuals with the variant: 1
Ethnicity/Population group: Western Europeanan, Central/Eastern European
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Pathogenic
(Feb 11, 2015)
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no assertion criteria provided
(clinical testing)
Method: clinical testing
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Breast-ovarian cancer, familial 1
Affected status: yes
Allele origin:
germline
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Institute of Human Genetics, Medical University Innsbruck
Study: BRCA-Tyrol
Accession: SCV000211996.1 First in ClinVar: Mar 03, 2015 Last updated: Mar 03, 2015
Comment:
BRCA-mutation spectrum Western Austria
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Number of individuals with the variant: 7
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Pathogenic
(Jan 31, 2014)
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no assertion criteria provided
Method: research
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Hereditary breast ovarian cancer syndrome
Affected status: yes
Allele origin:
germline
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Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV000587273.1 First in ClinVar: Aug 07, 2017 Last updated: Aug 07, 2017 |
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Pathogenic
(Dec 01, 2018)
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no assertion criteria provided
Method: research
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Ovarian neoplasm
Affected status: yes
Allele origin:
germline
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German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne
Accession: SCV000923977.1
First in ClinVar: Jun 17, 2019 Last updated: Jun 17, 2019 |
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Pathogenic
(Jun 11, 2019)
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no assertion criteria provided
Method: clinical testing
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Breast and/or ovarian cancer
Affected status: yes
Allele origin:
germline
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CZECANCA consortium
Accession: SCV001451823.1
First in ClinVar: Dec 26, 2020 Last updated: Dec 26, 2020 |
Number of individuals with the variant: 4
Ethnicity/Population group: Slavic
Geographic origin: Czech Republic
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Pathogenic
(Mar 02, 2020)
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no assertion criteria provided
Method: clinical testing
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Breast-ovarian cancer, familial, susceptibility to, 1
Affected status: yes
Allele origin:
germline
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BRCAlab, Lund University
Accession: SCV004244066.1
First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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The germline mutational landscape of BRCA1 and BRCA2 in Brazil. | Palmero EI | Scientific reports | 2018 | PMID: 29907814 |
Mutational spectrum in a worldwide study of 29,700 families with BRCA1 or BRCA2 mutations. | Rebbeck TR | Human mutation | 2018 | PMID: 29446198 |
Genetic Counselling, BRCA1/2 Status and Clinico-pathologic Characteristics of Patients with Ovarian Cancer before 50 Years of Age. | Cvelbar M | Radiology and oncology | 2017 | PMID: 28740454 |
Germline Mutation Status, Pathological Complete Response, and Disease-Free Survival in Triple-Negative Breast Cancer: Secondary Analysis of the GeparSixto Randomized Clinical Trial. | Hahnen E | JAMA oncology | 2017 | PMID: 28715532 |
High prevalence of BRCA1 stop mutation c.4183C>T in the Tyrolean population: implications for genetic testing. | Pölsler L | European journal of human genetics : EJHG | 2016 | PMID: 26014432 |
Novel BRCA1 and BRCA2 pathogenic mutations in Slovene hereditary breast and ovarian cancer families. | Novaković S | International journal of oncology | 2012 | PMID: 22923021 |
The occurrence of germline BRCA1 and BRCA2 sequence alterations in Slovenian population. | Stegel V | BMC medical genetics | 2011 | PMID: 21232165 |
Characterization of BRCA1 and BRCA2 deleterious mutations and variants of unknown clinical significance in unilateral and bilateral breast cancer: the WECARE study. | Borg A | Human mutation | 2010 | PMID: 20104584 |
BRCA1-related breast cancer in Austrian breast and ovarian cancer families: specific BRCA1 mutations and pathological characteristics. | Wagner TM | International journal of cancer | 1998 | PMID: 9663595 |
Text-mined citations for rs80357749 ...
HelpRecord last updated Nov 03, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.