5-156375070-T-G

Variant summary

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

The NM_000337.6(SGCD):c.192+30393T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,890 control chromosomes in the GnomAD database, including 20,799 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 0.52 (20799 hom., cov: 31)
• Consequence: SGCD NM_000337.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGCD	NM_000337.6	c.192+30393T>G		intron_variant		ENST00000337851.9
LOC124901120	XR_007059016.1	n.142+1058A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGCD	ENST00000337851.9	c.192+30393T>G		intron_variant		1	NM_000337.6	P4
SGCD	ENST00000435422.7	c.189+30393T>G		intron_variant		1		A1
SGCD	ENST00000517913.5	c.192+30393T>G		intron_variant		5
SGCD	ENST00000524347.2	c.193-18683T>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78288 AN: 151772 Hom.: 20789 Cov.: 31

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.516 AC: 78338 AN: 151890 Hom.: 20799 Cov.: 31 AF XY: 0.526 AC XY: 39081 AN XY: 74274

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.541

Alfa AF: 0.500 Hom.: 2805

Bravo AF: 0.508

Asia WGS AF: 0.755 AC: 2626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.4
Dann	Benign	0.75

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: rs970476; hg19: chr5-155802080;