ENST00000517913.5:c.-44+42879C>T

Variant names:

• chr5-156166898-C-T
• rs10866716
• ENST00000517913.5:c.-44+42879C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000517913.5(SGCD):​c.-44+42879C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,972 control chromosomes in the GnomAD database, including 25,568 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 0.56 (25568 hom., cov: 31)
• Consequence: SGCD ENST00000517913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585
• Publications: 0 publications found

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]

SGCD Gene-Disease associations (from GenCC):

• autosomal recessive limb-girdle muscular dystrophy

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• autosomal recessive limb-girdle muscular dystrophy type 2F

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Myriad Women’s Health, Ambry Genetics
• familial isolated dilated cardiomyopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• dilated cardiomyopathy

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• dilated cardiomyopathy 1L

  Inheritance: AD Classification: NO_KNOWN Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SGCD	XM_017009724.2	c.-44+42879C>T		intron_variant	Intron 2 of 9		XP_016865213.1
SGCD	XM_047417518.1	c.-44+42879C>T		intron_variant	Intron 4 of 11		XP_047273474.1
SGCD	XM_047417519.1	c.-44+42879C>T		intron_variant	Intron 3 of 10		XP_047273475.1
SGCD	XM_047417520.1	c.-1+42879C>T		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.-44+42879C>T		intron_variant	Intron 3 of 9	5		ENSP00000429378.1

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85626 AN: 151854 Hom.: 25560 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.564 AC: 85685 AN: 151972 Hom.: 25568 Cov.: 31 AF XY: 0.572 AC XY: 42449 AN XY: 74270

African (AFR) AF: 0.390 AC: 16155 AN: 41452

American (AMR) AF: 0.606 AC: 9253 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2061 AN: 3470

East Asian (EAS) AF: 0.940 AC: 4865 AN: 5178

South Asian (SAS) AF: 0.754 AC: 3627 AN: 4810

European-Finnish (FIN) AF: 0.615 AC: 6493 AN: 10562

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41239 AN: 67914

Other (OTH) AF: 0.565 AC: 1189 AN: 2106

Alfa AF: 0.604 Hom.: 14261

Bravo AF: 0.554

Asia WGS AF: 0.769 AC: 2673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.55
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10866716; hg19: chr5-155593908;