5-156326646-CTGTAATAAGCT-C

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The XR_007059016.1(LOC124901120):n.234+20796_234+20806del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0182 in 152,242 control chromosomes in the GnomAD database, including 313 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.018 (313 hom., cov: 33)
  • Exomes 𝑓: 0.038 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LOC124901120 XR_007059016.1 intron, non_coding_transcript
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: 2.15

Genes affected

LOC124901120 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

• BP6: Variant 5-156326646-CTGTAATAAGCT-C is Benign according to our data. Variant chr5-156326646-CTGTAATAAGCT-C is described in ClinVar as [Likely_benign]. Clinvar id is 556599.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901120	XR_007059016.1	n.234+20796_234+20806del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGCD	ENST00000517913.5	c.-43-2884_-43-2874del		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0183 AC: 2791 AN: 152126 Hom.: 317 Cov.: 33

Gnomad AFR AF: 0.00154

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0115

Gnomad ASJ AF: 0.00806

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.0742

Gnomad FIN AF: 0.0225

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00215

Gnomad OTH AF: 0.0181

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0385 AC: 1 AN: 26 Hom.: 0 AF XY: 0.0625 AC XY: 1 AN XY: 16

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0182 AC: 2775 AN: 152242 Hom.: 313 Cov.: 33 AF XY: 0.0224 AC XY: 1668 AN XY: 74410

Gnomad4 AFR AF: 0.00154

Gnomad4 AMR AF: 0.0113

Gnomad4 ASJ AF: 0.00806

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.0740

Gnomad4 FIN AF: 0.0225

Gnomad4 NFE AF: 0.00215

Gnomad4 OTH AF: 0.0175

Alfa AF: 0.00845 Hom.: 11

Bravo AF: 0.0176

Asia WGS AF: 0.156 AC: 539 AN: 3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Autosomal recessive limb-girdle muscular dystrophy type 2F Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Feb 08, 2023

- -

Autosomal recessive limb-girdle muscular dystrophy type 2F;C1847667:Dilated cardiomyopathy 1L Benign:1

Benign, criteria provided, single submitter

clinical testing

Counsyl

Feb 08, 2018

- -

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

May 26, 2021

- -

Dilated cardiomyopathy 1L Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Feb 08, 2023

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs149976574; hg19: chr5-155753656;