chr7-116525105-G-A
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001753.5(CAV1):c.30+13G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000628 in 1,608,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000027 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000066 ( 0 hom. )
Consequence
CAV1
NM_001753.5 intron
NM_001753.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.58
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 Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 7-116525105-G-A is Benign according to our data. Variant chr7-116525105-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2909499.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAV1 | NM_001753.5 | c.30+13G>A | intron_variant | ENST00000341049.7 | |||
CAV1 | NM_001172895.1 | c.-764G>A | 5_prime_UTR_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAV1 | ENST00000341049.7 | c.30+13G>A | intron_variant | 1 | NM_001753.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000272 AC: 4AN: 146884Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000445 AC: 11AN: 247274Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134256
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GnomAD4 exome AF: 0.0000664 AC: 97AN: 1461742Hom.: 0 Cov.: 31 AF XY: 0.0000660 AC XY: 48AN XY: 727172
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GnomAD4 genome AF: 0.0000272 AC: 4AN: 146988Hom.: 0 Cov.: 32 AF XY: 0.0000139 AC XY: 1AN XY: 71920
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Pulmonary hypertension, primary, 3 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 28, 2023 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at