rs17138767

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000462876.5(CAV2):​n.1007-146A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0721 in 152,276 control chromosomes in the GnomAD database, including 610 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 0.072 ( 610 hom., cov: 32)
Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

CAV2
ENST00000462876.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.16
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC107986838NR_188009.1 linkuse as main transcriptn.163+1731T>C intron_variant
LOC107986838NR_188010.1 linkuse as main transcriptn.163+1731T>C intron_variant
LOC107986838NR_188011.1 linkuse as main transcriptn.163+1731T>C intron_variant
LOC107986838NR_188012.1 linkuse as main transcriptn.163+1731T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CAV2ENST00000462876.5 linkuse as main transcriptn.1007-146A>G intron_variant 1
CAV2ENST00000467035.5 linkuse as main transcriptn.753-146A>G intron_variant 1
CAV2ENST00000472470.5 linkuse as main transcriptn.407-146A>G intron_variant 1

Frequencies

GnomAD3 genomes
AF:
0.0722
AC:
10985
AN:
152158
Hom.:
612
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0292
Gnomad AMI
AF:
0.0407
Gnomad AMR
AF:
0.0827
Gnomad ASJ
AF:
0.0343
Gnomad EAS
AF:
0.162
Gnomad SAS
AF:
0.121
Gnomad FIN
AF:
0.176
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.0727
Gnomad OTH
AF:
0.0544
GnomAD4 exome
AF:
0.500
AC:
1
AN:
2
Hom.:
0
AC XY:
0
AN XY:
0
show subpopulations
Gnomad4 NFE exome
AF:
0.500
GnomAD4 genome
AF:
0.0721
AC:
10982
AN:
152274
Hom.:
610
Cov.:
32
AF XY:
0.0774
AC XY:
5761
AN XY:
74448
show subpopulations
Gnomad4 AFR
AF:
0.0292
Gnomad4 AMR
AF:
0.0827
Gnomad4 ASJ
AF:
0.0343
Gnomad4 EAS
AF:
0.162
Gnomad4 SAS
AF:
0.121
Gnomad4 FIN
AF:
0.176
Gnomad4 NFE
AF:
0.0727
Gnomad4 OTH
AF:
0.0534
Alfa
AF:
0.0660
Hom.:
41
Bravo
AF:
0.0649
Asia WGS
AF:
0.111
AC:
386
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
9.4
DANN
Benign
0.73

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17138767; hg19: chr7-116137677; API