Variant chr7-116526346-C-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 ENST00000393467.1(CAV1):c.-242C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0738 in 1,477,908 control chromosomes in the GnomAD database, including 4,642 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.053 ( 312 hom., cov: 32)

Exomes 𝑓: 0.076 ( 4330 hom. )

Consequence

CAV1
ENST00000393467.1 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0640

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 7-116526346-C-T is Benign according to our data. Variant chr7-116526346-C-T is described in ClinVar as [Benign]. Clinvar id is 1275203.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.079 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
CAV1	NM_001753.5 linkuse as main transcript	c.31-179C>T	intron_variant	ENST00000341049.7
CAV1	NM_001172895.1 linkuse as main transcript	c.-63-179C>T	intron_variant
CAV1	NM_001172896.2 linkuse as main transcript		upstream_gene_variant
CAV1	NM_001172897.2 linkuse as main transcript		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAV1	ENST00000341049.7 linkuse as main transcript	c.31-179C>T		intron_variant		1	NM_001753.5	P3	Q03135-1

Frequencies

GnomAD3 genomes

AF:

0.0535

AC:

8134

AN:

152126

Hom.:

312

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0155

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.0452

Gnomad ASJ

AF:

0.0655

Gnomad EAS

AF:

0.000580

Gnomad SAS

AF:

0.0195

Gnomad FIN

AF:

0.0664

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0808

Gnomad OTH

AF:

0.0678

GnomAD4 exome

AF:

0.0761

AC:

100934

AN:

1325666

Hom.:

4330

Cov.:

AF XY:

0.0747

AC XY:

48440

AN XY:

648524

show subpopulations

Gnomad4 AFR exome

AF:

0.0126

Gnomad4 AMR exome

AF:

0.0472

Gnomad4 ASJ exome

AF:

0.0666

Gnomad4 EAS exome

AF:

0.0000867

Gnomad4 SAS exome

AF:

0.0221

Gnomad4 FIN exome

AF:

0.0672

Gnomad4 NFE exome

AF:

0.0860

Gnomad4 OTH exome

AF:

0.0678

GnomAD4 genome

AF:

0.0534

AC:

8130

AN:

152242

Hom.:

312

Cov.:

AF XY:

0.0510

AC XY:

3792

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.0154

Gnomad4 AMR

AF:

0.0452

Gnomad4 ASJ

AF:

0.0655

Gnomad4 EAS

AF:

0.000581

Gnomad4 SAS

AF:

0.0197

Gnomad4 FIN

AF:

0.0664

Gnomad4 NFE

AF:

0.0808

Gnomad4 OTH

AF:

0.0671

Alfa

AF:

0.0676

Hom.:

Bravo

AF:

0.0525

Asia WGS

AF:

0.0100

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 30, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Benign

0.90

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