rs249878

chr5-156218241-G-Achr5-156218241-G-C

Variant summary

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

The ENST00000517913.5(SGCD):c.-44+94222G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,020 control chromosomes in the GnomAD database, including 2,658 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 0.16 (2658 hom., cov: 32)
• Consequence: SGCD ENST00000517913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

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 (NFE) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGCD	XM_017009724.2	c.-44+94222G>A		intron_variant
SGCD	XM_047417518.1	c.-44+94222G>A		intron_variant
SGCD	XM_047417519.1	c.-44+94222G>A		intron_variant
SGCD	XM_047417520.1	c.-1+94222G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGCD	ENST00000517913.5	c.-44+94222G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24917 AN: 151900 Hom.: 2660 Cov.: 32

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0733

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.164 AC: 24923 AN: 152020 Hom.: 2658 Cov.: 32 AF XY: 0.165 AC XY: 12271 AN XY: 74302

Gnomad4 AFR AF: 0.0434

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0734

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.148

Alfa AF: 0.192 Hom.: 428

Bravo AF: 0.156

Asia WGS AF: 0.113 AC: 396 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	2.6
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs249878; hg19: chr5-155645251;