ClinVar Genomic variation as it relates to human health
NM_001198800.3(ASCC1):c.626+1G>A
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_001198800.3(ASCC1):c.626+1G>A
Variation ID: 619021 Accession: VCV000619021.11
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 10q22.1 10: 72161537 (GRCh38) [ NCBI UCSC ] 10: 73921295 (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 Aug 14, 2019 Mar 18, 2023 Aug 15, 2022 - HGVS
- ... more HGVS ... less HGVS
- Protein change
- Other names
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- Canonical SPDI
- NC_000010.11:72161536:C:T
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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
Help
The frequency of the allele represented by this VCV record.
The Genome Aggregation Database (gnomAD) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Exome Aggregation Consortium (ExAC) 0.00002
- 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
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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ASCC1 | - | - |
GRCh38 GRCh37 |
179 | 195 |
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 (3) |
criteria provided, multiple submitters, no conflicts
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Jul 10, 2020 | RCV000791458.4 | |
Pathogenic (1) |
criteria provided, single submitter
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Jun 28, 2019 | RCV001004046.1 | |
Pathogenic (1) |
criteria provided, single submitter
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Jun 28, 2019 | RCV000855457.1 | |
Likely pathogenic (3) |
criteria provided, single submitter
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Aug 15, 2022 | RCV001796204.3 |
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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Pathogenic
(Dec 01, 2018)
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criteria provided, single submitter
Method: clinical testing
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Spinal muscular atrophy with congenital bone fractures 2
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Laboratory Genomica, Gynecology and Assisted Reproduction Hospital Malinov DM
Accession: SCV000882722.1
First in ClinVar: Aug 14, 2019 Last updated: Aug 14, 2019 |
Clinical Features:
Areflexia (present) , Multiple prenatal fractures (present) , Cryptorchidism (present) , Respiratory distress (present)
Age: 0-9 years
Sex: male
Geographic origin: Bulgaria
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Pathogenic
(Jun 28, 2019)
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criteria provided, single submitter
Method: research
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Arthrogryposis multiplex congenita
Fetal akinesia sequence
Affected status: yes
Allele origin:
inherited
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Cirak Lab, University Hospital Cologne
Accession: SCV000996587.1
First in ClinVar: Nov 08, 2019 Last updated: Nov 08, 2019 |
Number of individuals with the variant: 1
Sex: female
Ethnicity/Population group: Turkish
Geographic origin: Turkey
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Pathogenic
(Jun 28, 2019)
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criteria provided, single submitter
Method: clinical testing
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Pena-Shokeir syndrome type I
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
inherited
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Cirak Lab, University Hospital Cologne
Accession: SCV000951630.1
First in ClinVar: Feb 27, 2020 Last updated: Feb 27, 2020 |
Clinical Features:
Fetal akinesia deformation sequence 1 (present)
Sex: female
Ethnicity/Population group: Turkish
Geographic origin: Turkey
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Pathogenic
(Jul 10, 2020)
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criteria provided, single submitter
Method: clinical testing
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SPINAL MUSCULAR ATROPHY WITH CONGENITAL BONE FRACTURES 2
Affected status: yes
Allele origin:
germline
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Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
Accession: SCV001984831.1
First in ClinVar: Oct 30, 2021 Last updated: Oct 30, 2021 |
Comment:
This variant affects the canonical splice donor site of intron 7 of 12, and is therefore predicted to interfere with splicing and result in loss … (more)
This variant affects the canonical splice donor site of intron 7 of 12, and is therefore predicted to interfere with splicing and result in loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay (NMD). This variant has been previously reported as a homozygous change (c.626+1G>A using an alternative transcript NM_001198800.2) in patients with fetal akinesia (PMID: 28749478, 31680123). It is present in the heterozygous state in the gnomAD population database at a frequency of 0.002% (6/251412) and thus is presumed to be rare. Based on the available evidence, the c.710+1G>A variant is classified as Pathogenic. (less)
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Likely pathogenic
(Aug 15, 2022)
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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: SCV003805953.1
First in ClinVar: Mar 04, 2023 Last updated: Mar 04, 2023 |
Comment:
Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; … (more)
Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; Also known as c.710+1 G>A; This variant is associated with the following publications: (PMID: 31680123, 34136434, 34426522, 28749478) (less)
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
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: SCV002035098.1 First in ClinVar: Dec 18, 2021 Last updated: Dec 18, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV002037450.1 First in ClinVar: Dec 18, 2021 Last updated: Dec 18, 2021 |
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Pathogenic
(Jan 01, 2023)
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no assertion criteria provided
Method: clinical testing
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Spinal muscular atrophy with congenital bone fractures 2
Affected status: no
Allele origin:
germline
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Payam Genetics Center, General Welfare Department of North Khorasan Province
Accession: SCV003842179.1
First in ClinVar: Mar 18, 2023 Last updated: Mar 18, 2023 |
Age: 0-9 years
Sex: male
Ethnicity/Population group: Iranian
Geographic origin: Iran
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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 genomic and clinical landscape of fetal akinesia. | Pergande M | Genetics in medicine : official journal of the American College of Medical Genetics | 2020 | PMID: 31680123 |
Molecular autopsy in maternal-fetal medicine. | Shamseldin HE | Genetics in medicine : official journal of the American College of Medical Genetics | 2018 | PMID: 28749478 |
Clinical spectrum and diagnostic criteria of infantile spinal muscular atrophy: further delineation on the basis of SMN gene deletion findings. | Rudnik-Schöneborn S | Neuropediatrics | 1996 | PMID: 8677029 |
Text-mined citations for rs747595523 ...
HelpRecord last updated Dec 17, 2023
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.