rs17138765

Positions:

• chr7-116497472-G-A

Variant summary

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

The ENST00000462876.5(CAV2):​n.1007-297G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,212 control chromosomes in the GnomAD database, including 973 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 0.10 (973 hom., cov: 32)
• Consequence: CAV2 ENST00000462876.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

Genes affected

CAV2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986838	NR_188009.1	n.163+1882C>T		intron_variant
LOC107986838	NR_188010.1	n.163+1882C>T		intron_variant
LOC107986838	NR_188011.1	n.163+1882C>T		intron_variant
LOC107986838	NR_188012.1	n.163+1882C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAV2	ENST00000462876.5	n.1007-297G>A		intron_variant		1
CAV2	ENST00000467035.5	n.753-297G>A		intron_variant		1
CAV2	ENST00000472470.5	n.407-297G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15519 AN: 152096 Hom.: 967 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0701

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0216

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.102 AC: 15547 AN: 152212 Hom.: 973 Cov.: 32 AF XY: 0.0980 AC XY: 7295 AN XY: 74414

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0699

Gnomad4 ASJ AF: 0.0899

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0212

Gnomad4 FIN AF: 0.0651

Gnomad4 NFE AF: 0.0845

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0889 Hom.: 126

Bravo AF: 0.108

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17138765; hg19: chr7-116137526;