NM_000023.4(SGCA):c.408C>T (p.Ala136=) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(2);Uncertain significance(1) (Last evaluated: Jun 1, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000347845.3

Allele description [Variation Report for NM_000023.4(SGCA):c.408C>T (p.Ala136=)]

NM_000023.4(SGCA):c.408C>T (p.Ala136=)

Gene:
SGCA:sarcoglycan alpha [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q21.33
Genomic location:
Preferred name:
NM_000023.4(SGCA):c.408C>T (p.Ala136=)
HGVS:
  • NC_000017.11:g.50168396C>T
  • NG_008889.1:g.7392C>T
  • NM_000023.4:c.408C>TMANE SELECT
  • NM_001135697.3:c.408C>T
  • NP_000014.1:p.Ala136=
  • NP_001129169.1:p.Ala136=
  • LRG_203t1:c.408C>T
  • LRG_203:g.7392C>T
  • NC_000017.10:g.48245757C>T
  • NM_000023.2:c.408C>T
  • NR_135553.2:n.444C>T
  • p.Ala136Ala
Links:
dbSNP: rs143551687
NCBI 1000 Genomes Browser:
rs143551687
Molecular consequence:
  • NR_135553.2:n.444C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000023.4:c.408C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001135697.3:c.408C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000341906EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Uncertain significance
(May 24, 2016)
germlineclinical testing

Citation Link,

SCV000969748GeneDxcriteria provided, single submitter
Likely benign
(Jun 1, 2018)
germlineclinical testing

Citation Link,

SCV001433784ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratoriescriteria provided, single submitter
Likely benign
(May 27, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000341906.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000969748.1

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

Description

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 a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories, SCV001433784.1

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

Description

The p.Ala136Ala variant (rs143551687) does not alter the amino acid sequence of the SGCA protein and computational splice site prediction algorithms do not predict a change in the nearest splice site or creation of a cryptic splice site. This variant has not been reported in association with cardiomyopathy in medical literature or in gene specific variation databases. This variant is listed in the Genome Aggregation Database (gnomAD) with a frequency of 0.07 percent in the East Asian population (identified on 17 out of 25,998 chromosomes) and has been reported to the ClinVar database (Variation ID: 287947). Based on these observations, the p.Ala136Ala variant is likely to be benign.

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

Last Updated: May 26, 2021

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