rs17138767

Variant summary

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

The ENST00000446355.2(ENSG00000237813):​n.112+1731T>C variant causes a intron, non coding transcript 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


ENST00000446355.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.16
Variant links:
Genes affected
CAV2 (HGNC:1528): (caveolin 2) The protein encoded by this gene is a major component of the inner surface of caveolae, small invaginations of the plasma membrane, and is involved in essential cellular functions, including signal transduction, lipid metabolism, cellular growth control and apoptosis. This protein may function as a tumor suppressor. This gene and related family member (CAV1) are located next to each other on chromosome 7, and express colocalizing proteins that form a stable hetero-oligomeric complex. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. Additional isoforms resulting from the use of alternate in-frame translation initiation codons have also been described, and shown to have preferential localization in the cell (PMID:11238462). [provided by RefSeq, May 2011]

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

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000446355.2 linkuse as main transcriptn.112+1731T>C intron_variant, non_coding_transcript_variant 5

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