rs8713
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001753.5(CAV1):c.*456A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 433,510 control chromosomes in the GnomAD database, including 6,984 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 0.19 ( 3204 hom., cov: 32)
Exomes 𝑓: 0.15 ( 3780 hom. )
Consequence
CAV1
NM_001753.5 3_prime_UTR
NM_001753.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.354
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAV1 | NM_001753.5 | c.*456A>C | 3_prime_UTR_variant | 3/3 | ENST00000341049.7 | ||
CAV1 | NM_001172895.1 | c.*456A>C | 3_prime_UTR_variant | 3/3 | |||
CAV1 | NM_001172896.2 | c.*456A>C | 3_prime_UTR_variant | 2/2 | |||
CAV1 | NM_001172897.2 | c.*456A>C | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAV1 | ENST00000341049.7 | c.*456A>C | 3_prime_UTR_variant | 3/3 | 1 | NM_001753.5 | P3 | ||
CAV1 | ENST00000393467.1 | c.*456A>C | 3_prime_UTR_variant | 2/2 | 1 | A1 | |||
CAV1 | ENST00000405348.6 | c.*456A>C | 3_prime_UTR_variant | 3/3 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.191 AC: 28979AN: 151920Hom.: 3201 Cov.: 32
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GnomAD4 exome AF: 0.152 AC: 42644AN: 281472Hom.: 3780 Cov.: 0 AF XY: 0.152 AC XY: 21847AN XY: 143542
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GnomAD4 genome ? AF: 0.191 AC: 29019AN: 152038Hom.: 3204 Cov.: 32 AF XY: 0.184 AC XY: 13676AN XY: 74326
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at