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NM_000337.6(SGCD):c.510G>A (p.Glu170=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(4);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 15, 2020
Accession:
VCV000352335.10
Variation ID:
352335
Description:
single nucleotide variant
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NM_000337.6(SGCD):c.510G>A (p.Glu170=)

Allele ID
302804
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q33.3
Genomic location
5: 156647471 (GRCh38) GRCh38 UCSC
5: 156074481 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_205:g.782128G>A
LRG_205t1:c.510G>A LRG_205p1:p.Glu170=
NC_000005.9:g.156074481G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000005.10:156647470:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00029
Exome Aggregation Consortium (ExAC) 0.00053
1000 Genomes Project 0.00060
Trans-Omics for Precision Medicine (TOPMed) 0.00026
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00016
Links
ClinGen: CA3530620
dbSNP: rs368838376
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 Jun 14, 2016 RCV000282447.2
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV000392260.2
Likely benign 1 criteria provided, single submitter May 20, 2013 RCV000619731.1
Benign 1 criteria provided, single submitter Jan 10, 2017 RCV000424458.1
Likely benign 1 criteria provided, single submitter Apr 28, 2017 RCV000770208.1
Likely benign 1 criteria provided, single submitter Nov 15, 2020 RCV001084791.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jun 3, 2019 RCV000731143.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SGCD - - GRCh38
GRCh37
493 509

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Limb-Girdle Muscular Dystrophy, Recessive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000455495.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jan 10, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000514617.4
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)
Uncertain significance
(Dec 29, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000858921.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Apr 28, 2017)
criteria provided, single submitter
Method: clinical testing
Cardiomyopathy
Allele origin: germline
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario
Study: Canadian Open Genetics Repository
Accession: SCV000901638.1
Submitted: (Apr 30, 2018)
Evidence details
Benign
(Jun 03, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001145592.1
Submitted: (Sep 25, 2019)
Evidence details
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Qualitative or quantitative defects of delta-sarcoglycan
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000455494.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(May 20, 2013)
criteria provided, single submitter
Method: clinical testing
Cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000739879.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, … (more)
Likely benign
(Nov 15, 2020)
criteria provided, single submitter
Method: clinical testing
Autosomal recessive limb-girdle muscular dystrophy type 2F
Allele origin: germline
Invitae
Accession: SCV000761130.4
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=SGCD - - - -

Text-mined citations for rs368838376...

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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 Nov 27, 2021