rs3807992
Variant names:
Variant summary
Our verdict is Benign. The variant received -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
NM_001753.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.472
Publications
44 publications found
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]
CAV1 Gene-Disease associations (from GenCC):
- pulmonary arterial hypertensionInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- partial lipodystrophy, congenital cataracts, and neurodegeneration syndromeInheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- pulmonary hypertension, primary, 3Inheritance: AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- congenital generalized lipodystrophy type 3Inheritance: AD, AR Classification: MODERATE, LIMITED Submitted by: Ambry Genetics, G2P
- heritable pulmonary arterial hypertensionInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Berardinelli-Seip congenital lipodystrophyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- amyotrophic lateral sclerosisInheritance: AD Classification: LIMITED Submitted by: ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAV1 | NM_001753.5 | c.196-1755G>A | intron_variant | Intron 2 of 2 | ENST00000341049.7 | NP_001744.2 | ||
CAV1 | NM_001172895.1 | c.103-1755G>A | intron_variant | Intron 2 of 2 | NP_001166366.1 | |||
CAV1 | NM_001172896.2 | c.103-1755G>A | intron_variant | Intron 1 of 1 | NP_001166367.1 | |||
CAV1 | NM_001172897.2 | c.103-1755G>A | intron_variant | Intron 2 of 2 | NP_001166368.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.278 AC: 42223AN: 152044Hom.: 6141 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
42223
AN:
152044
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.278 AC: 42265AN: 152162Hom.: 6143 Cov.: 32 AF XY: 0.276 AC XY: 20563AN XY: 74398 show subpopulations
GnomAD4 genome
AF:
AC:
42265
AN:
152162
Hom.:
Cov.:
32
AF XY:
AC XY:
20563
AN XY:
74398
show subpopulations
African (AFR)
AF:
AC:
15133
AN:
41474
American (AMR)
AF:
AC:
3488
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
865
AN:
3470
East Asian (EAS)
AF:
AC:
1141
AN:
5182
South Asian (SAS)
AF:
AC:
1252
AN:
4818
European-Finnish (FIN)
AF:
AC:
2950
AN:
10606
Middle Eastern (MID)
AF:
AC:
74
AN:
294
European-Non Finnish (NFE)
AF:
AC:
16557
AN:
68002
Other (OTH)
AF:
AC:
550
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1579
3158
4736
6315
7894
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
428
856
1284
1712
2140
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
765
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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