rs9314059

Positions:

• chr5-156707324-A-G

Variant summary

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

The NM_000337.6(SGCD):​c.576-50257A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0307 in 152,264 control chromosomes in the GnomAD database, including 155 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 0.031 (155 hom., cov: 33)
• Consequence: SGCD NM_000337.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.07 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGCD	NM_000337.6	c.576-50257A>G		intron_variant		ENST00000337851.9
LOC105377673	XR_007059015.1	n.627-3049T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGCD	ENST00000337851.9	c.576-50257A>G		intron_variant		1	NM_000337.6	P4
SGCD	ENST00000435422.7	c.573-50257A>G		intron_variant		1		A1
	ENST00000520705.1	n.243-3049T>C		intron_variant, non_coding_transcript_variant		3
SGCD	ENST00000517913.5	c.576-50257A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0307 AC: 4664 AN: 152146 Hom.: 154 Cov.: 33

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0200

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0354

Gnomad FIN AF: 0.00772

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0307 AC: 4674 AN: 152264 Hom.: 155 Cov.: 33 AF XY: 0.0298 AC XY: 2217 AN XY: 74468

Gnomad4 AFR AF: 0.0722

Gnomad4 AMR AF: 0.0200

Gnomad4 ASJ AF: 0.0311

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0358

Gnomad4 FIN AF: 0.00772

Gnomad4 NFE AF: 0.0137

Gnomad4 OTH AF: 0.0251

Alfa AF: 0.0248 Hom.: 19

Bravo AF: 0.0326

Asia WGS AF: 0.0210 AC: 72 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.69

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: rs9314059; hg19: chr5-156134335;