rs10491465

chr5-156653954-G-T

Variant summary

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

The NM_000337.6(SGCD):c.575+6418G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0311 in 152,156 control chromosomes in the GnomAD database, including 166 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 0.031 (166 hom., cov: 31)
• Consequence: SGCD NM_000337.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGCD	NM_000337.6	c.575+6418G>T		intron_variant		ENST00000337851.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGCD	ENST00000337851.9	c.575+6418G>T		intron_variant		1	NM_000337.6	P4
SGCD	ENST00000435422.7	c.572+6418G>T		intron_variant		1		A1
SGCD	ENST00000517913.5	c.575+6418G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0310 AC: 4710 AN: 152036 Hom.: 163 Cov.: 31

Gnomad AFR AF: 0.0792

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0205

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.00830

Gnomad FIN AF: 0.00764

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0124

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0311 AC: 4735 AN: 152156 Hom.: 166 Cov.: 31 AF XY: 0.0297 AC XY: 2209 AN XY: 74388

Gnomad4 AFR AF: 0.0795

Gnomad4 AMR AF: 0.0206

Gnomad4 ASJ AF: 0.0236

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.00851

Gnomad4 FIN AF: 0.00764

Gnomad4 NFE AF: 0.0124

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.0160 Hom.: 36

Bravo AF: 0.0342

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.0
Dann	Benign	0.72

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: rs10491465; hg19: chr5-156080965;