rs1394606

chr5-156332836-C-T

Variant summary

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

The NM_000337.6(SGCD):c.3+3257C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0904 in 152,180 control chromosomes in the GnomAD database, including 812 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 0.090 (812 hom., cov: 32)
• Consequence: SGCD NM_000337.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593

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]

LOC124901120 (HGNC:):

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 = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGCD	NM_000337.6	c.3+3257C>T		intron_variant		ENST00000337851.9
LOC124901120	XR_007059016.1	n.234+14617G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGCD	ENST00000337851.9	c.3+3257C>T		intron_variant		1	NM_000337.6	P4
SGCD	ENST00000435422.7	c.-1+5604C>T		intron_variant		1		A1
SGCD	ENST00000517913.5	c.3+3257C>T		intron_variant		5
SGCD	ENST00000524347.2	c.3+3257C>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0905 AC: 13769 AN: 152064 Hom.: 814 Cov.: 32

Gnomad AFR AF: 0.0291

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.0850

Gnomad ASJ AF: 0.0952

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0848

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0941

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

GnomAD4 genome AF: 0.0904 AC: 13759 AN: 152180 Hom.: 812 Cov.: 32 AF XY: 0.0910 AC XY: 6769 AN XY: 74402

Gnomad4 AFR AF: 0.0291

Gnomad4 AMR AF: 0.0848

Gnomad4 ASJ AF: 0.0952

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0846

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.0931

Alfa AF: 0.118 Hom.: 1553

Bravo AF: 0.0808

Asia WGS AF: 0.0400 AC: 138 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	0.26
Dann	Benign	0.43

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: rs1394606; hg19: chr5-155759846;