rs7632287

Positions:

• chr3-8749760-G-A

Variant summary

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

The ENST00000472766.1(CAV3):​n.155+15770G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,142 control chromosomes in the GnomAD database, including 9,045 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 0.31 (9045 hom., cov: 33)
• Consequence: CAV3 ENST00000472766.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

Genes affected

CAV3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OXTR	XR_007095681.1	n.1884+3124C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAV3	ENST00000472766.1	n.155+15770G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46912 AN: 152024 Hom.: 9023 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.0682

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.309 AC: 46987 AN: 152142 Hom.: 9045 Cov.: 33 AF XY: 0.302 AC XY: 22465 AN XY: 74378

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0112

Gnomad4 SAS AF: 0.0680

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.283

Alfa AF: 0.257 Hom.: 3340

Bravo AF: 0.315

Asia WGS AF: 0.0890 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7632287; hg19: chr3-8791446;