ClinVar Genomic variation as it relates to human health
NM_000535.7(PMS2):c.706-4del
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000535.7(PMS2):c.706-4del
Variation ID: 218461 Accession: VCV000218461.33
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 7p22.1 7: 5997427 (GRCh38) [ NCBI UCSC ] 7: 6037058 (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 Dec 27, 2015 Feb 28, 2024 Jan 25, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000535.7:c.706-4del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
intron variant NM_000535.5:c.706-4delT NM_000535.5:c.706-5delT NM_000535.6:c.706-4delT NM_000535.6:c.706-5delT NM_001322003.2:c.301-4del intron variant NM_001322004.2:c.301-4del intron variant NM_001322005.2:c.301-4del intron variant NM_001322006.2:c.706-4del intron variant NM_001322007.2:c.388-4del intron variant NM_001322008.2:c.388-4del intron variant NM_001322009.2:c.301-4del intron variant NM_001322010.2:c.301-4del intron variant NM_001322011.2:c.-228-4del intron variant NM_001322012.2:c.-228-4del intron variant NM_001322013.2:c.133-4del intron variant NM_001322014.2:c.706-4del intron variant NM_001322015.2:c.397-4del intron variant NC_000007.14:g.5997443del NC_000007.13:g.6037074del NG_008466.1:g.16680del LRG_161:g.16680del LRG_161t1:c.706-4del - Protein change
- Other names
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- Canonical SPDI
- NC_000007.14:5997426:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA
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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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0.00326 (AAAAAAAAAAAAAA)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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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
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
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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PMS2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
5163 | 5257 |
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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Benign (2) |
criteria provided, single submitter
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Jul 10, 2015 | RCV000203188.2 | |
Benign (5) |
criteria provided, multiple submitters, no conflicts
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May 28, 2019 | RCV000415703.8 | |
Benign/Likely benign (5) |
criteria provided, multiple submitters, no conflicts
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Aug 15, 2023 | RCV000454744.12 | |
Benign (2) |
criteria provided, multiple submitters, no conflicts
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Oct 6, 2021 | RCV000564416.7 | |
Benign (1) |
criteria provided, single submitter
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Jan 1, 2019 | RCV001262162.2 | |
Benign (2) |
criteria provided, multiple submitters, no conflicts
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Sep 23, 2022 | RCV001689733.3 | |
Benign (1) |
criteria provided, single submitter
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Jan 25, 2024 | RCV001520436.7 | |
Benign (1) |
criteria provided, single submitter
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May 2, 2019 | RCV001798676.3 |
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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Benign
(Jul 10, 2015)
|
criteria provided, single submitter
Method: clinical testing
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Lynch syndrome
Affected status: unknown
Allele origin:
unknown
|
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia
Accession: SCV000257707.2
First in ClinVar: Dec 27, 2015 Last updated: Dec 27, 2015 |
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Benign
(Apr 17, 2015)
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criteria provided, single submitter
Method: clinical testing
|
Lynch syndrome
Affected status: unknown
Allele origin:
unknown
|
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia
Accession: SCV000257705.2
First in ClinVar: Dec 27, 2015 Last updated: Dec 27, 2015 |
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Benign
(Mar 28, 2016)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
|
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000540065.1
First in ClinVar: Apr 09, 2017 Last updated: Apr 09, 2017 |
Comment:
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or … (more)
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency (less)
Method: Genome/Exome Filtration
|
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Benign
(Jun 28, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
Lynch syndrome 4
Affected status: yes
Allele origin:
germline
|
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Study: VKGL Data-share Consensus
Accession: SCV000745197.1 First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018 |
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Benign
(May 28, 2019)
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criteria provided, single submitter
Method: clinical testing
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Lynch syndrome 4
Affected status: unknown
Allele origin:
unknown
|
Mendelics
Accession: SCV001137318.1
First in ClinVar: Jan 09, 2020 Last updated: Jan 09, 2020 |
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Benign
(Jan 01, 2019)
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criteria provided, single submitter
Method: clinical testing
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Ovarian neoplasm
Affected status: yes
Allele origin:
unknown
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Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV001439935.1
First in ClinVar: Oct 31, 2020 Last updated: Oct 31, 2020 |
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Benign
(Dec 15, 2017)
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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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GeneDx
Accession: SCV001911041.1
First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
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Benign
(May 02, 2019)
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criteria provided, single submitter
Method: clinical testing
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Breast and/or ovarian cancer
Affected status: unknown
Allele origin:
germline
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CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario
Accession: SCV002042815.1
First in ClinVar: Jan 01, 2022 Last updated: Jan 01, 2022 |
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Benign
(May 18, 2017)
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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: SCV000663426.4
First in ClinVar: Jan 01, 2018 Last updated: Mar 04, 2023 |
Comment:
General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Number of individuals with the variant: 1
|
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Likely benign
(Aug 15, 2023)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital
Accession: SCV002568042.4
First in ClinVar: Sep 03, 2022 Last updated: Aug 18, 2023 |
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Benign
(Sep 23, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV001470605.2
First in ClinVar: Jan 26, 2021 Last updated: Jan 06, 2024 |
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Benign
(Oct 06, 2021)
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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: SCV000691102.3
First in ClinVar: Feb 19, 2018 Last updated: Feb 14, 2024 |
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Benign
(Jan 25, 2024)
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criteria provided, single submitter
Method: clinical testing
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Hereditary nonpolyposis colorectal neoplasms
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV001729530.4
First in ClinVar: Jun 15, 2021 Last updated: Feb 28, 2024 |
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Uncertain significance
(Oct 23, 2015)
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no assertion criteria provided
Method: clinical testing
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Lynch syndrome 4
Affected status: no
Allele origin:
germline
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Knight Diagnostic Laboratories, Oregon Health and Sciences University
Study: CSER-NextGen
Accession: SCV000493782.1 First in ClinVar: Jan 23, 2017 Last updated: Jan 23, 2017 |
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Benign
(-)
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no assertion criteria provided
Method: clinical testing
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Lynch syndrome 4
Affected status: yes
Allele origin:
germline
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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV000734566.1 First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018 |
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Likely benign
(Apr 22, 2015)
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no assertion criteria provided
Method: clinical testing
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Lynch syndrome 4
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV000745847.1 First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018 |
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Benign
(-)
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no assertion criteria provided
Method: clinical testing
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not specified
Affected status: yes
Allele origin:
unknown
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Department of Pathology and Laboratory Medicine, Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001553089.1 First in ClinVar: Apr 13, 2021 Last updated: Apr 13, 2021 |
Comment:
GnomAD population frequency 44%
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Benign
(-)
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no assertion criteria provided
Method: clinical testing
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not specified
Affected status: yes
Allele origin:
germline
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Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001799646.1 First in ClinVar: Aug 21, 2021 Last updated: Aug 21, 2021 |
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Benign
(-)
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no assertion criteria provided
Method: clinical testing
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not specified
Affected status: yes
Allele origin:
germline
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Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001905791.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
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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
HelpThere are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for rs60794673 ...
HelpRecord last updated Jun 17, 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.