Variant chr5-156326739-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The ENST00000517913.5(SGCD):c.-43-2795C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0129 in 152,528 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.013 ( 22 hom., cov: 33)

Exomes 𝑓: 0.0085 ( 0 hom. )

Consequence

SGCD
ENST00000517913.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.965

Variant links:

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 links:

LOC124901120 (HGNC:):

LOC124901120 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 5-156326739-C-A is Benign according to our data. Variant chr5-156326739-C-A is described in ClinVar as [Benign]. Clinvar id is 1183373.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0129 (1972/152292) while in subpopulation SAS AF= 0.0184 (89/4828). AF 95% confidence interval is 0.0153. There are 22 homozygotes in gnomad4. There are 997 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 22 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein	UniProt
SGCD	XM_017009724.2 link	c.-43-2795C>A	intron_variant	XP_016865213.1	Q92629-2
SGCD	XM_047417518.1 link	c.-43-2795C>A	intron_variant	XP_047273474.1
SGCD	XM_047417519.1 link	c.-43-2795C>A	intron_variant	XP_047273475.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SGCD	ENST00000517913.5 link	c.-43-2795C>A		intron_variant		5		ENSP00000429378.1		Q92629-3
SGCD	ENST00000435422.7 link	c.-494C>A		upstream_gene_variant		1		ENSP00000403003.2		Q92629-1

Frequencies

GnomAD3 genomes

AF:

0.0129

AC:

1959

AN:

152174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0122

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0115

Gnomad ASJ

AF:

0.0199

Gnomad EAS

AF:

0.0141

Gnomad SAS

AF:

0.0178

Gnomad FIN

AF:

0.0142

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0127

Gnomad OTH

AF:

0.0124

GnomAD4 exome

AF:

0.00847

AC:

AN:

236

Hom.:

Cov.:

AF XY:

0.0118

AC XY:

AN XY:

170

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0145

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0129

AC:

1972

AN:

152292

Hom.:

Cov.:

AF XY:

0.0134

AC XY:

997

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.0124

Gnomad4 AMR

AF:

0.0115

Gnomad4 ASJ

AF:

0.0199

Gnomad4 EAS

AF:

0.0141

Gnomad4 SAS

AF:

0.0184

Gnomad4 FIN

AF:

0.0142

Gnomad4 NFE

AF:

0.0127

Gnomad4 OTH

AF:

0.0123

Alfa

AF:

0.0126

Hom.:

Bravo

AF:

0.0123

Asia WGS

AF:

0.0200

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.81

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over