rs17138756

Positions:

• chr7-116495199-A-G

Variant summary

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

The ENST00000462876.5(CAV2):​n.1007-2570A>G 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 152,170 control chromosomes in the GnomAD database, including 967 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 (967 hom., cov: 32)
• Consequence: CAV2 ENST00000462876.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.938

Genes affected

CAV2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986838	NR_188009.1	n.163+4155T>C		intron_variant
LOC107986838	NR_188010.1	n.163+4155T>C		intron_variant
LOC107986838	NR_188011.1	n.163+4155T>C		intron_variant
LOC107986838	NR_188012.1	n.163+4155T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAV2	ENST00000462876.5	n.1007-2570A>G		intron_variant		1
CAV2	ENST00000467035.5	n.753-2570A>G		intron_variant		1
CAV2	ENST00000472470.5	n.407-2570A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15460 AN: 152052 Hom.: 961 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.0679

Gnomad ASJ AF: 0.0900

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0215

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0844

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.102 AC: 15488 AN: 152170 Hom.: 967 Cov.: 32 AF XY: 0.0976 AC XY: 7263 AN XY: 74420

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0677

Gnomad4 ASJ AF: 0.0900

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0211

Gnomad4 FIN AF: 0.0650

Gnomad4 NFE AF: 0.0844

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0902 Hom.: 1299

Bravo AF: 0.108

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	13
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17138756; hg19: chr7-116135253;