NM_000070.3(CAPN3):c.495C>T (p.Phe165=) AND Limb-girdle muscular dystrophy, type 2A

Clinical significance:Benign/Likely benign (Last evaluated: Dec 5, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000559703.6

Allele description [Variation Report for NM_000070.3(CAPN3):c.495C>T (p.Phe165=)]

NM_000070.3(CAPN3):c.495C>T (p.Phe165=)

Gene:
CAPN3:calpain 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q15.1
Genomic location:
Preferred name:
NM_000070.3(CAPN3):c.495C>T (p.Phe165=)
HGVS:
  • NC_000015.10:g.42386282C>T
  • NG_008660.1:g.43180C>T
  • NM_000070.3:c.495C>TMANE SELECT
  • NM_024344.2:c.495C>T
  • NM_173087.2:c.495C>T
  • NP_000061.1:p.Phe165=
  • NP_077320.1:p.Phe165=
  • NP_775110.1:p.Phe165=
  • LRG_849t1:c.495C>T
  • LRG_849:g.43180C>T
  • LRG_849p1:p.Phe165=
  • NC_000015.9:g.42678480C>T
  • NM_000070.2:c.495C>T
  • NP_000061.1:p.(=)
Links:
dbSNP: rs1801324
NCBI 1000 Genomes Browser:
rs1801324
Molecular consequence:
  • NM_000070.3:c.495C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_024344.2:c.495C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_173087.2:c.495C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Limb-girdle muscular dystrophy, type 2A (LGMDR1)
Synonyms:
Limb-girdle muscular dystrophy type 2; Muscular dystrophy, pelvofemoral; Leyden-Moebius muscular dystrophy; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009675; MedGen: C1869123; Orphanet: 267; OMIM: 253600

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000645503Invitaecriteria provided, single submitter
Benign
(Dec 5, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001274230Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Likely benign
(Apr 27, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000645503.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Clinical Services Laboratory,Illumina, SCV001274230.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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