chr5-156326904-C-G

Position:

• chr5-156326904-C-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000435422.7(SGCD):​c.-329C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0759 in 152,334 control chromosomes in the GnomAD database, including 454 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.076 (454 hom., cov: 33)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: SGCD ENST00000435422.7 5_prime_UTR
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:2
• Conservation: PhyloP100: -1.50

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 5-156326904-C-G is Benign according to our data. Variant chr5-156326904-C-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 48112.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=2}.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901120	XR_007059016.1	n.234+20549G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGCD	ENST00000435422.7	c.-329C>G		5_prime_UTR_variant	1/8	1		A1
SGCD	ENST00000517913.5	c.-43-2630C>G		intron_variant		5
SGCD	ENST00000524347.2			upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.0758 AC: 11528 AN: 152146 Hom.: 454 Cov.: 33

Gnomad AFR AF: 0.0783

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0449

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0717

Gnomad OTH AF: 0.0836

GnomAD4 exome AF: 0.100 AC: 7 AN: 70 Hom.: 0 Cov.: 0 AF XY: 0.0962 AC XY: 5 AN XY: 52

Gnomad4 AFR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.103

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0759 AC: 11552 AN: 152264 Hom.: 454 Cov.: 33 AF XY: 0.0773 AC XY: 5758 AN XY: 74454

Gnomad4 AFR AF: 0.0782

Gnomad4 AMR AF: 0.0816

Gnomad4 ASJ AF: 0.0836

Gnomad4 EAS AF: 0.0472

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.0449

Gnomad4 NFE AF: 0.0717

Gnomad4 OTH AF: 0.0827

Alfa AF: 0.0334 Hom.: 15

Bravo AF: 0.0761

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1 Benign:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Qualitative or quantitative defects of delta-sarcoglycan Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Apr 20, 2012

- -

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	-0.86
CADD	Benign	0.30
DANN	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.12		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: rs7717393; hg19: chr5-155753914;