Variant chr7-116525106-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001753.5(CAV1):c.30+14G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0139 in 1,614,164 control chromosomes in the GnomAD database, including 416 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 22 hom., cov: 33)

Exomes 𝑓: 0.014 ( 394 hom. )

Consequence

CAV1
NM_001753.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.221

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]

CAV1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 7-116525106-G-T is Benign according to our data. Variant chr7-116525106-G-T is described in ClinVar as [Benign]. Clinvar id is 379541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-116525106-G-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAV1	NM_001753.5 linkuse as main transcript	c.30+14G>T		intron_variant		ENST00000341049.7
CAV1	NM_001172895.1 linkuse as main transcript	c.-763G>T		5_prime_UTR_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAV1	ENST00000341049.7 linkuse as main transcript	c.30+14G>T		intron_variant		1	NM_001753.5	P3	Q03135-1

Frequencies

GnomAD3 genomes

AF:

0.0111

AC:

1692

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00398

Gnomad AMI

AF:

0.0493

Gnomad AMR

AF:

0.0100

Gnomad ASJ

AF:

0.0179

Gnomad EAS

AF:

0.00367

Gnomad SAS

AF:

0.0737

Gnomad FIN

AF:

0.00141

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0124

Gnomad OTH

AF:

0.0129

GnomAD3 exomes

AF:

0.0172

AC:

4299

AN:

249718

Hom.:

125

AF XY:

0.0201

AC XY:

2719

AN XY:

135130

show subpopulations

Gnomad AFR exome

AF:

0.00427

Gnomad AMR exome

AF:

0.0115

Gnomad ASJ exome

AF:

0.0224

Gnomad EAS exome

AF:

0.00299

Gnomad SAS exome

AF:

0.0708

Gnomad FIN exome

AF:

0.00180

Gnomad NFE exome

AF:

0.0110

Gnomad OTH exome

AF:

0.0179

GnomAD4 exome

AF:

0.0142

AC:

20702

AN:

1461868

Hom.:

394

Cov.:

AF XY:

0.0160

AC XY:

11662

AN XY:

727232

show subpopulations

Gnomad4 AFR exome

AF:

0.00385

Gnomad4 AMR exome

AF:

0.0111

Gnomad4 ASJ exome

AF:

0.0222

Gnomad4 EAS exome

AF:

0.00622

Gnomad4 SAS exome

AF:

0.0674

Gnomad4 FIN exome

AF:

0.00234

Gnomad4 NFE exome

AF:

0.0110

Gnomad4 OTH exome

AF:

0.0152

GnomAD4 genome

AF:

0.0111

AC:

1689

AN:

152296

Hom.:

Cov.:

AF XY:

0.0118

AC XY:

877

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.00397

Gnomad4 AMR

AF:

0.0100

Gnomad4 ASJ

AF:

0.0179

Gnomad4 EAS

AF:

0.00367

Gnomad4 SAS

AF:

0.0737

Gnomad4 FIN

AF:

0.00141

Gnomad4 NFE

AF:

0.0124

Gnomad4 OTH

AF:

0.0119

Alfa

AF:

0.00940

Hom.:

Bravo

AF:

0.00966

Asia WGS

AF:

0.0400

AC:

139

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 31, 2015

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Pulmonary hypertension, primary, 3

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 30, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

5.5

DANN

Benign

0.88

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over