NM_000231.3:c.228T>C

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000231.3(SGCG):c.228T>C(p.Asp76Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 1,610,324 control chromosomes in the GnomAD database, including 13,336 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1990 hom., cov: 32)

Exomes 𝑓: 0.12 ( 11346 hom. )

Consequence

SGCG
NM_000231.3 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:12

Conservation

PhyloP100: 1.46

Variant links:

Genes affected

SGCG (HGNC:10809): (sarcoglycan gamma) This gene encodes gamma-sarcoglycan, one of several sarcolemmal transmembrane glycoproteins that interact with dystrophin. The dystrophin-glycoprotein complex (DGC) spans the sarcolemma and is comprised of dystrophin, syntrophin, alpha- and beta-dystroglycans and sarcoglycans. The DGC provides a structural link between the subsarcolemmal cytoskeleton and the extracellular matrix of muscle cells. Defects in the encoded protein can lead to early onset autosomal recessive muscular dystrophy, in particular limb-girdle muscular dystrophy, type 2C (LGMD2C). [provided by RefSeq, Oct 2008]

SGCG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 13-23234643-T-C is Benign according to our data. Variant chr13-23234643-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 92653.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-23234643-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=1.46 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SGCG	NM_000231.3 link	c.228T>C	p.Asp76Asp	synonymous_variant	Exon 3 of 8	ENST00000218867.4	NP_000222.2	Q13326

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGCG	ENST00000218867.4 link	c.228T>C	p.Asp76Asp	synonymous_variant	Exon 3 of 8	1	NM_000231.3	ENSP00000218867.3		Q13326

Frequencies

GnomAD3 genomes

AF:

0.147

AC:

22276

AN:

151854

Hom.:

1988

Cov.:

show subpopulations

Gnomad AFR

AF:

0.249

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.102

Gnomad ASJ

AF:

0.125

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.0780

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.130

GnomAD3 exomes

AF:

0.105

AC:

26294

AN:

251362

Hom.:

1823

AF XY:

0.104

AC XY:

14163

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.253

Gnomad AMR exome

AF:

0.0573

Gnomad ASJ exome

AF:

0.131

Gnomad EAS exome

AF:

0.000815

Gnomad SAS exome

AF:

0.102

Gnomad FIN exome

AF:

0.0795

Gnomad NFE exome

AF:

0.118

Gnomad OTH exome

AF:

0.106

GnomAD4 exome

AF:

0.118

AC:

172428

AN:

1458354

Hom.:

11346

Cov.:

AF XY:

0.117

AC XY:

84883

AN XY:

725660

show subpopulations

Gnomad4 AFR exome

AF:

0.252

Gnomad4 AMR exome

AF:

0.0614

Gnomad4 ASJ exome

AF:

0.129

Gnomad4 EAS exome

AF:

0.000429

Gnomad4 SAS exome

AF:

0.101

Gnomad4 FIN exome

AF:

0.0843

Gnomad4 NFE exome

AF:

0.124

Gnomad4 OTH exome

AF:

0.120

GnomAD4 genome

AF:

0.147

AC:

22283

AN:

151970

Hom.:

1990

Cov.:

AF XY:

0.141

AC XY:

10438

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.248

Gnomad4 AMR

AF:

0.102

Gnomad4 ASJ

AF:

0.125

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.101

Gnomad4 FIN

AF:

0.0780

Gnomad4 NFE

AF:

0.122

Gnomad4 OTH

AF:

0.128

Alfa

AF:

0.132

Hom.:

1104

Bravo

AF:

0.154

Asia WGS

AF:

0.0640

AC:

224

AN:

3478

EpiCase

AF:

0.118

EpiControl

AF:

0.118

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:12

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Feb 02, 2016

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Aug 16, 2012

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 15, 2013

Genetic Services Laboratory, University of Chicago

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 26, 2014

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

p.Asp76Asp in exon 3 of SGCG: This variant is not expected to have clinical sign ificance because it has been identified in 24% (1040/4406) of African American c hromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/E VS/; dbSNP rs1800350). -

Autosomal recessive limb-girdle muscular dystrophy type 2C

Benign:3

Jul 01, 2021

Pars Genome Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 16, 2020

Natera, Inc.

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Apr 14, 2017

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Limb-girdle muscular dystrophy, recessive

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sarcoglycanopathy

Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

3.7

DANN

Benign

0.44

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over