VCV000130200.36 - ClinVar

NM_014363.6(SACS):c.10338G>A (p.Gln3446=)

Germline

Classification

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.

(14)

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.

Benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_014363.6(SACS):c.10338G>A (p.Gln3446=)

Variation ID: 130200 Accession: VCV000130200.36

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 13q12.12 13: 23333538 (GRCh38) [ NCBI UCSC ] 13: 23907677 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	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	Jul 6, 2014	Sep 29, 2024	Feb 1, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_014363.6:c.10338G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_055178.3:p.Gln3446=	synonymous
NM_001278055.2:c.9897G>A	NP_001264984.1:p.Gln3299=	synonymous
NC_000013.11:g.23333538C>T
NC_000013.10:g.23907677C>T
NG_012342.1:g.105165G>A

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000013.11:23333537:C:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The 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.

0.01458 (C)

Allele frequency Help The frequency of the allele represented by this VCV record.

1000 Genomes Project 30x 0.98407

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.98439

Trans-Omics for Precision Medicine (TOPMed) 0.98490

1000 Genomes Project 0.98542

The Genome Aggregation Database (gnomAD) 0.98600

Exome Aggregation Consortium (ExAC) 0.99566

The Genome Aggregation Database (gnomAD), exomes 0.99644

Links

ClinGen: CA155038 dbSNP: rs2737701 VarSome

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
Gene	OMIM	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.
SACS		-	-	GRCh38 GRCh37	4111	4313

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.
not specified	Benign (4)	criteria provided, multiple submitters, no conflicts	Sep 20, 2019	RCV000118229.17
Charlevoix-Saguenay spastic ataxia	Benign (5)	criteria provided, multiple submitters, no conflicts	Jul 1, 2021	RCV000270430.13
not provided	Benign (3)	criteria provided, multiple submitters, no conflicts	Jul 5, 2018	RCV000676352.9
Hereditary spastic paraplegia	Benign (1)	criteria provided, single submitter	Dec 12, 2016	RCV001847717.4
Spastic paraplegia	Benign (1)	criteria provided, single submitter	Feb 1, 2024	RCV001509973.8

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.
Benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	NOT SPECIFIED Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV000312143.1 First in ClinVar: Oct 02, 2016 Last updated: Oct 02, 2016
Benign (Sep 21, 2015)	criteria provided, single submitter (ACGS Guidelines, 2013) Method: clinical testing	Charlevoix-Saguenay spastic ataxia Affected status: yes Allele origin: germline	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center Study: VKGL Data-share Consensus Accession: SCV000745004.1 First in ClinVar: Apr 19, 2018 Last updated: Apr 19, 2018
Benign (Sep 20, 2019)	criteria provided, single submitter (Athena Diagnostics Criteria) Method: clinical testing	not specified Affected status: unknown Allele origin: unknown	Athena Diagnostics Accession: SCV001475434.1 First in ClinVar: Jan 26, 2021 Last updated: Jan 26, 2021
Benign (Dec 12, 2016)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Hereditary spastic paraplegia Affected status: yes Allele origin: germline	Genome Diagnostics Laboratory, The Hospital for Sick Children Accession: SCV002104955.1 First in ClinVar: Mar 19, 2022 Last updated: Mar 19, 2022
Benign (Jun 14, 2016)	criteria provided, single submitter (ICSL Variant Classification 20161018) Method: clinical testing	ARSACS Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV000383311.2 First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016
Benign (Jul 01, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Charlevoix-Saguenay spastic ataxia Affected status: no Allele origin: germline	Genome-Nilou Lab Accession: SCV001750102.1 First in ClinVar: Jul 15, 2021 Last updated: Jul 15, 2021	Sex: mixed
Benign (Jul 05, 2018)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV001869867.1 First in ClinVar: Sep 19, 2021 Last updated: Sep 19, 2021
Benign (Feb 01, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Spastic paraplegia Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001716894.4 First in ClinVar: Jun 15, 2021 Last updated: Feb 14, 2024
Benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: not provided	not provided (Autosomal recessive inheritance) Affected status: yes Allele origin: germline	Breakthrough Genomics, Breakthrough Genomics Accession: SCV005230844.1 First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024
Likely benign (-)	no assertion criteria provided Method: clinical testing	AllHighlyPenetrant (Autosomal recessive inheritance) Affected status: unknown Allele origin: germline	Genetic Services Laboratory, University of Chicago Accession: SCV000152588.2 First in ClinVar: May 17, 2014 Last updated: Jul 06, 2014	Comment: Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more) Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. (less)
Benign (-)	no assertion criteria provided Method: clinical testing	Charlevoix-Saguenay spastic ataxia Affected status: yes Allele origin: germline	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen Study: VKGL Data-share Consensus Accession: SCV000733201.1 First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018
Benign (Feb 19, 2016)	no assertion criteria provided Method: clinical testing	not provided Affected status: unknown Allele origin: unknown	Mayo Clinic Laboratories, Mayo Clinic Accession: SCV000802126.1 First in ClinVar: Aug 05, 2018 Last updated: Aug 05, 2018
Benign (-)	no assertion criteria provided Method: clinical testing	not specified Affected status: yes Allele origin: germline	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: SCV001957076.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021
Benign (Nov 16, 2019)	no assertion criteria provided Method: clinical testing	Charlevoix-Saguenay type spastic ataxia Affected status: unknown Allele origin: germline	Natera, Inc. Accession: SCV002086177.1 First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022
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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

There 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 rs2737701 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_014363.6(SACS):c.10338G>A (p.Gln3446=)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs2737701 ...