rs12530912

Variant summary

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

The ENST00000446355.2(ENSG00000237813):​n.113-4572A>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 0.252 in 152,190 control chromosomes in the GnomAD database, including 4,932 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 0.25 ( 4932 hom., cov: 33)

Consequence


ENST00000446355.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.546
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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000446355.2 linkuse as main transcriptn.113-4572A>C intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.252
AC:
38295
AN:
152072
Hom.:
4924
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.283
Gnomad AMI
AF:
0.198
Gnomad AMR
AF:
0.235
Gnomad ASJ
AF:
0.291
Gnomad EAS
AF:
0.172
Gnomad SAS
AF:
0.291
Gnomad FIN
AF:
0.242
Gnomad MID
AF:
0.269
Gnomad NFE
AF:
0.240
Gnomad OTH
AF:
0.239
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.252
AC:
38329
AN:
152190
Hom.:
4932
Cov.:
33
AF XY:
0.253
AC XY:
18807
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.283
Gnomad4 AMR
AF:
0.235
Gnomad4 ASJ
AF:
0.291
Gnomad4 EAS
AF:
0.172
Gnomad4 SAS
AF:
0.291
Gnomad4 FIN
AF:
0.242
Gnomad4 NFE
AF:
0.240
Gnomad4 OTH
AF:
0.236
Alfa
AF:
0.247
Hom.:
2242
Bravo
AF:
0.254
Asia WGS
AF:
0.192
AC:
670
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
6.6
DANN
Benign
0.74

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: rs12530912; hg19: chr7-116127529; API