rs6875111

Positions:

• chr5-155826870-G-A

Variant summary

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

The XM_017009724.2(SGCD):​c.-208+97880G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,156 control chromosomes in the GnomAD database, including 2,146 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 0.12 (2146 hom., cov: 33)
• Consequence: SGCD XM_017009724.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SGCD	XM_017009724.2	c.-208+97880G>A		intron_variant			XP_016865213.1
SGCD	XM_047417518.1	c.-344-43474G>A		intron_variant			XP_047273474.1
SGCD	XM_047417519.1	c.-288-43474G>A		intron_variant			XP_047273475.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17715 AN: 152038 Hom.: 2141 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.0793

Gnomad AMR AF: 0.0646

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.0899

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0298

Gnomad OTH AF: 0.0979

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

GnomAD4 genome AF: 0.117 AC: 17742 AN: 152156 Hom.: 2146 Cov.: 33 AF XY: 0.115 AC XY: 8545 AN XY: 74388

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.0645

Gnomad4 ASJ AF: 0.0473

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.0898

Gnomad4 FIN AF: 0.0249

Gnomad4 NFE AF: 0.0297

Gnomad4 OTH AF: 0.0988

Alfa AF: 0.0474 Hom.: 728

Bravo AF: 0.131

Asia WGS AF: 0.161 AC: 557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
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: rs6875111; hg19: chr5-155253880;