rs1368329

chr5-155947735-C-T

Variant summary

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

The ENST00000517913.5(SGCD):c.-282+77311C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 151,980 control chromosomes in the GnomAD database, including 3,373 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 0.19 (3373 hom., cov: 31)
• Consequence: SGCD ENST00000517913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGCD	XM_017009724.2	c.-207-176121C>T		intron_variant
SGCD	XM_047417518.1	c.-264+77311C>T		intron_variant
SGCD	XM_047417519.1	c.-208+77311C>T		intron_variant
SGCD	XM_047417520.1	c.-164-176121C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGCD	ENST00000517913.5	c.-282+77311C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29056 AN: 151862 Hom.: 3357 Cov.: 31

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.0667

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.191 AC: 29086 AN: 151980 Hom.: 3373 Cov.: 31 AF XY: 0.191 AC XY: 14214 AN XY: 74278

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.0655

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.217

Alfa AF: 0.198 Hom.: 707

Bravo AF: 0.216

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.71
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1368329; hg19: chr5-155374745;