rs10052410

Variant names:

• chr5-156287334-T-C
• rs10052410
• ENST00000517913.5:c.-43-42200T>C

Variant summary

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

The ENST00000517913.5(SGCD):​c.-43-42200T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,866 control chromosomes in the GnomAD database, including 13,957 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 0.41 (13957 hom., cov: 32)
• Consequence: SGCD ENST00000517913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SGCD	XM_017009724.2	c.-43-42200T>C		intron_variant	Intron 2 of 9		XP_016865213.1
SGCD	XM_047417518.1	c.-43-42200T>C		intron_variant	Intron 4 of 11		XP_047273474.1
SGCD	XM_047417519.1	c.-43-42200T>C		intron_variant	Intron 3 of 10		XP_047273475.1
SGCD	XM_047417520.1	c.1-57155T>C		intron_variant	Intron 2 of 8		XP_047273476.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGCD	ENST00000517913.5	c.-43-42200T>C		intron_variant	Intron 3 of 9	5		ENSP00000429378.1

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62415 AN: 151750 Hom.: 13951 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.0834

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.411 AC: 62469 AN: 151866 Hom.: 13957 Cov.: 32 AF XY: 0.405 AC XY: 30046 AN XY: 74194

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.0836

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.377

Alfa AF: 0.365 Hom.: 20502

Bravo AF: 0.418

Asia WGS AF: 0.184 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10052410; hg19: chr5-155714344;