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

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 4, 2020
Accession:
VCV000287947.4
Variation ID:
287947
Description:
single nucleotide variant
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NM_000023.4(SGCA):c.408C>T (p.Ala136=)

Allele ID
272184
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q21.33
Genomic location
17: 50168396 (GRCh38) GRCh38 UCSC
17: 48245757 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.48245757C>T
NC_000017.11:g.50168396C>T
NM_000023.4:c.408C>T MANE Select NP_000014.1:p.Ala136= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000017.11:50168395:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00004
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Exome Aggregation Consortium (ExAC) 0.00038
The Genome Aggregation Database (gnomAD), exomes 0.00013
1000 Genomes Project 0.00020
Links
ClinGen: CA8643797
dbSNP: rs143551687
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Nov 4, 2020 RCV001426063.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Jun 1, 2018 RCV000347845.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SGCA - - GRCh38
GRCh37
405 418

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(May 24, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000341906.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Jun 01, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000969748.1
Submitted: (Apr 12, 2019)
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
(May 27, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV001433784.1
Submitted: (Oct 10, 2018)
Evidence details
Comment:
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 … (more)
Likely benign
(Nov 04, 2020)
criteria provided, single submitter
Method: clinical testing
Autosomal recessive limb-girdle muscular dystrophy type 2D
Allele origin: germline
Invitae
Accession: SCV001628708.1
Submitted: (Jan 07, 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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SGCA - - - -

Text-mined citations for rs143551687...

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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 May 26, 2021