rs237917

Variant names:

• chr3-8771013-T-C
• rs237917
• ENST00000472766.1:n.156-6464T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-8771013-T-C
• chr3-8771013-T-G

Variant summary

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

The ENST00000472766.1(CAV3):​n.156-6464T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 151,624 control chromosomes in the GnomAD database, including 33,491 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 0.66 (33491 hom., cov: 32)
• Consequence: CAV3 ENST00000472766.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

Genes affected

CAV3 (HGNC:1529): (caveolin 3) This gene encodes a caveolin family member, which functions as a component of the caveolae plasma membranes found in most cell types. Caveolin proteins are proposed to be scaffolding proteins for organizing and concentrating certain caveolin-interacting molecules. Mutations identified in this gene lead to interference with protein oligomerization or intra-cellular routing, disrupting caveolae formation and resulting in Limb-Girdle muscular dystrophy type-1C (LGMD-1C), hyperCKemia or rippling muscle disease (RMD). Alternative splicing has been identified for this locus, with inclusion or exclusion of a differentially spliced intron. In addition, transcripts utilize multiple polyA sites and contain two potential translation initiation sites. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAV3	ENST00000472766.1	n.156-6464T>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99364 AN: 151506 Hom.: 33481 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.656 AC: 99413 AN: 151624 Hom.: 33491 Cov.: 32 AF XY: 0.649 AC XY: 48106 AN XY: 74086

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.684

Alfa AF: 0.591 Hom.: 2008

Bravo AF: 0.645

Asia WGS AF: 0.480 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.4
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs237917; hg19: chr3-8812699;