rs931798

chr5-156383813-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000337.6(SGCD):c.192+39136A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 152,110 control chromosomes in the GnomAD database, including 48,412 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (48412 hom., cov: 31)
• Consequence: SGCD NM_000337.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

SGCD (HGNC:10807): (sarcoglycan delta) The protein encoded by this gene is one of the four known components of the sarcoglycan complex, which is a subcomplex of the dystrophin-glycoprotein complex (DGC). DGC forms a link between the F-actin cytoskeleton and the extracellular matrix. This protein is expressed most abundantly in skeletal and cardiac muscle. Mutations in this gene have been associated with autosomal recessive limb-girdle muscular dystrophy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding distinct isoforms have been observed for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGCD	NM_000337.6	c.192+39136A>G		intron_variant		ENST00000337851.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGCD	ENST00000337851.9	c.192+39136A>G		intron_variant		1	NM_000337.6	P4
SGCD	ENST00000435422.7	c.189+39136A>G		intron_variant		1		A1
SGCD	ENST00000517913.5	c.192+39136A>G		intron_variant		5
SGCD	ENST00000524347.2	c.193-9940A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120277 AN: 151994 Hom.: 48361 Cov.: 31

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.801

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.791 AC: 120389 AN: 152110 Hom.: 48412 Cov.: 31 AF XY: 0.795 AC XY: 59090 AN XY: 74334

Gnomad4 AFR AF: 0.935

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.803

Alfa AF: 0.743 Hom.: 10555

Bravo AF: 0.801

Asia WGS AF: 0.882 AC: 3065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.28
Dann	Benign	0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs931798; hg19: chr5-155810823;