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NM_000070.3(CAPN3):c.984C>T (p.Cys328=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Aug 19, 2021)
Last evaluated:
Dec 5, 2020
Accession:
VCV000166787.7
Variation ID:
166787
Description:
single nucleotide variant
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NM_000070.3(CAPN3):c.984C>T (p.Cys328=)

Allele ID
177546
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q15.1
Genomic location
15: 42392677 (GRCh38) GRCh38 UCSC
15: 42684875 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_849:g.49575C>T
LRG_849t1:c.984C>T LRG_849p1:p.Cys328=
NC_000015.10:g.42392677C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000015.10:42392676:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00160 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00582
Trans-Omics for Precision Medicine (TOPMed) 0.00589
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00623
Exome Aggregation Consortium (ExAC) 0.00635
The Genome Aggregation Database (gnomAD) 0.00570
1000 Genomes Project 0.00160
Links
ClinGen: CA179838
dbSNP: rs28364441
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Nov 18, 2016 RCV000152921.6
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Dec 5, 2020 RCV000538067.7
Likely benign 1 no assertion criteria provided - RCV001573447.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CAPN3 - - GRCh38
GRCh37
999 1011

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000301902.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Nov 18, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000521446.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Limb-girdle muscular dystrophy, type 2A
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001277568.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (2)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
Limb-girdle muscular dystrophy, type 2A
Allele origin: germline
Invitae
Accession: SCV000645521.5
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jan 27, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000202350.7
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Limb-girdle muscular dystrophy type 2A
Allele origin: germline
Natera, Inc.
Accession: SCV001454332.1
Submitted: (Dec 28, 2020)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001799351.1
Submitted: (Aug 19, 2021)
Evidence details

Functional evidence

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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 this variant

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Title Author Journal Year Link
Correlations between clinical severity, genotype and muscle pathology in limb girdle muscular dystrophy type 2A. Fanin M Journal of medical genetics 2007 PMID: 17526799
Screening of calpain-3 autolytic activity in LGMD muscle: a functional map of CAPN3 gene mutations. Fanin M Journal of medical genetics 2007 PMID: 16971480
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CAPN3 - - - -

Text-mined citations for rs28364441...

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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 18, 2021