Variant 7-116525179-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 NM_001753.5(CAV1):c.30+87C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.052 in 1,613,894 control chromosomes in the GnomAD database, including 2,568 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.048 ( 175 hom., cov: 33)

Exomes 𝑓: 0.052 ( 2393 hom. )

Consequence

CAV1
NM_001753.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.460

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=-0.85).

BP6

Variant 7-116525179-C-T is Benign according to our data. Variant chr7-116525179-C-T is described in ClinVar as [Benign]. Clinvar id is 1232819.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0831 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+87C>T		intron_variant		ENST00000341049.7
CAV1	NM_001172895.1 linkuse as main transcript	c.-690C>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+87C>T		intron_variant		1	NM_001753.5	P3	Q03135-1

Frequencies

GnomAD3 genomes

AF:

0.0478

AC:

7272

AN:

152148

Hom.:

175

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0406

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.0347

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.0890

Gnomad FIN

AF:

0.0243

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0547

Gnomad OTH

AF:

0.0578

GnomAD3 exomes

AF:

0.0480

AC:

11833

AN:

246388

Hom.:

420

AF XY:

0.0520

AC XY:

6963

AN XY:

134000

show subpopulations

Gnomad AFR exome

AF:

0.0383

Gnomad AMR exome

AF:

0.0253

Gnomad ASJ exome

AF:

0.117

Gnomad EAS exome

AF:

0.000871

Gnomad SAS exome

AF:

0.0843

Gnomad FIN exome

AF:

0.0246

Gnomad NFE exome

AF:

0.0524

Gnomad OTH exome

AF:

0.0530

GnomAD4 exome

AF:

0.0524

AC:

76650

AN:

1461628

Hom.:

2393

Cov.:

AF XY:

0.0544

AC XY:

39558

AN XY:

727106

show subpopulations

Gnomad4 AFR exome

AF:

0.0409

Gnomad4 AMR exome

AF:

0.0266

Gnomad4 ASJ exome

AF:

0.123

Gnomad4 EAS exome

AF:

0.000378

Gnomad4 SAS exome

AF:

0.0854

Gnomad4 FIN exome

AF:

0.0245

Gnomad4 NFE exome

AF:

0.0525

Gnomad4 OTH exome

AF:

0.0550

GnomAD4 genome

AF:

0.0478

AC:

7279

AN:

152266

Hom.:

175

Cov.:

AF XY:

0.0461

AC XY:

3431

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.0406

Gnomad4 AMR

AF:

0.0346

Gnomad4 ASJ

AF:

0.117

Gnomad4 EAS

AF:

0.00155

Gnomad4 SAS

AF:

0.0901

Gnomad4 FIN

AF:

0.0243

Gnomad4 NFE

AF:

0.0547

Gnomad4 OTH

AF:

0.0572

Alfa

AF:

0.0563

Hom.:

135

Bravo

AF:

0.0459

Asia WGS

AF:

0.0370

AC:

129

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 06, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

9.9

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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