3-8749653-G-T

Position:

• chr3-8749653-G-T

Variant summary

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

The ENST00000472766.1(CAV3):​n.155+15663G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,168 control chromosomes in the GnomAD database, including 1,316 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 0.13 (1316 hom., cov: 33)
• Consequence: CAV3 ENST00000472766.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

Genes affected

CAV3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OXTR	XR_007095681.1	n.1884+3231C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAV3	ENST00000472766.1	n.155+15663G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19212 AN: 152050 Hom.: 1313 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0994

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0279

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.126 AC: 19234 AN: 152168 Hom.: 1316 Cov.: 33 AF XY: 0.122 AC XY: 9095 AN XY: 74402

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0994

Gnomad4 ASJ AF: 0.0652

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0280

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0968 Hom.: 236

Bravo AF: 0.132

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11720238; hg19: chr3-8791339;