rs3807992

Variant summary

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

The NM_001753.5(CAV1):​c.196-1755G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,162 control chromosomes in the GnomAD database, including 6,143 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 0.28 ( 6143 hom., cov: 32)

Consequence

CAV1
NM_001753.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.472
Variant links:
Genes affected
CAV1 (HGNC:1527): (caveolin 1) The scaffolding protein encoded by this gene is the main component of the caveolae plasma membranes found in most cell types. The protein links integrin subunits to the tyrosine kinase FYN, an initiating step in coupling integrins to the Ras-ERK pathway and promoting cell cycle progression. The gene is a tumor suppressor gene candidate and a negative regulator of the Ras-p42/44 mitogen-activated kinase cascade. Caveolin 1 and caveolin 2 are located next to each other on chromosome 7 and express colocalizing proteins that form a stable hetero-oligomeric complex. Mutations in this gene have been associated with Berardinelli-Seip congenital lipodystrophy. Alternatively spliced transcripts encode alpha and beta isoforms of caveolin 1.[provided by RefSeq, Mar 2010]

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=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CAV1NM_001753.5 linkuse as main transcriptc.196-1755G>A intron_variant ENST00000341049.7
CAV1NM_001172895.1 linkuse as main transcriptc.103-1755G>A intron_variant
CAV1NM_001172896.2 linkuse as main transcriptc.103-1755G>A intron_variant
CAV1NM_001172897.2 linkuse as main transcriptc.103-1755G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CAV1ENST00000341049.7 linkuse as main transcriptc.196-1755G>A intron_variant 1 NM_001753.5 P3Q03135-1

Frequencies

GnomAD3 genomes
AF:
0.278
AC:
42223
AN:
152044
Hom.:
6141
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.365
Gnomad AMI
AF:
0.280
Gnomad AMR
AF:
0.228
Gnomad ASJ
AF:
0.249
Gnomad EAS
AF:
0.220
Gnomad SAS
AF:
0.261
Gnomad FIN
AF:
0.278
Gnomad MID
AF:
0.247
Gnomad NFE
AF:
0.243
Gnomad OTH
AF:
0.263
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.278
AC:
42265
AN:
152162
Hom.:
6143
Cov.:
32
AF XY:
0.276
AC XY:
20563
AN XY:
74398
show subpopulations
Gnomad4 AFR
AF:
0.365
Gnomad4 AMR
AF:
0.228
Gnomad4 ASJ
AF:
0.249
Gnomad4 EAS
AF:
0.220
Gnomad4 SAS
AF:
0.260
Gnomad4 FIN
AF:
0.278
Gnomad4 NFE
AF:
0.243
Gnomad4 OTH
AF:
0.260
Alfa
AF:
0.252
Hom.:
648
Bravo
AF:
0.279
Asia WGS
AF:
0.219
AC:
765
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.6
DANN
Benign
0.42

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs3807992; hg19: chr7-116197245; API