Variant chr9-100578087-G-A 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_001018116.2(CAVIN4):c.-57G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 1,589,798 control chromosomes in the GnomAD database, including 130,540 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 11237 hom., cov: 32)

Exomes 𝑓: 0.40 ( 119303 hom. )

Consequence

CAVIN4
NM_001018116.2 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 2.58

Variant links:

Genes affected

CAVIN4 (HGNC:33742): (caveolae associated protein 4) This gene encodes a protein containing two coiled-coil regions. The encoded protein promotes Rho/ROCK (Rho-kinase) signaling in cardiac muscles cells, and may facilitate myofibrillar organization. [provided by RefSeq, Jun 2013]

CAVIN4 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=-0.5).

BP6

Variant 9-100578087-G-A is Benign according to our data. Variant chr9-100578087-G-A is described in ClinVar as [Benign]. Clinvar id is 674700.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
CAVIN4	NM_001018116.2 linkuse as main transcript	c.-57G>A	5_prime_UTR_variant	1/2	ENST00000307584.6
CAVIN4	XM_047423346.1 linkuse as main transcript	c.22-102G>A	intron_variant
CAVIN4	XM_047423347.1 linkuse as main transcript	c.21+1132G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAVIN4	ENST00000307584.6 linkuse as main transcript	c.-57G>A		5_prime_UTR_variant	1/2	1	NM_001018116.2	P1

Frequencies

GnomAD3 genomes

AF:

0.374

AC:

56861

AN:

151890

Hom.:

11226

Cov.:

show subpopulations

Gnomad AFR

AF:

0.299

Gnomad AMI

AF:

0.480

Gnomad AMR

AF:

0.452

Gnomad ASJ

AF:

0.433

Gnomad EAS

AF:

0.0909

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.409

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.418

Gnomad OTH

AF:

0.387

GnomAD4 exome

AF:

0.401

AC:

576776

AN:

1437790

Hom.:

119303

Cov.:

AF XY:

0.399

AC XY:

286052

AN XY:

716674

show subpopulations

Gnomad4 AFR exome

AF:

0.292

Gnomad4 AMR exome

AF:

0.515

Gnomad4 ASJ exome

AF:

0.430

Gnomad4 EAS exome

AF:

0.0739

Gnomad4 SAS exome

AF:

0.340

Gnomad4 FIN exome

AF:

0.403

Gnomad4 NFE exome

AF:

0.417

Gnomad4 OTH exome

AF:

0.384

GnomAD4 genome

AF:

0.374

AC:

56923

AN:

152008

Hom.:

11237

Cov.:

AF XY:

0.375

AC XY:

27827

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.299

Gnomad4 AMR

AF:

0.453

Gnomad4 ASJ

AF:

0.433

Gnomad4 EAS

AF:

0.0909

Gnomad4 SAS

AF:

0.331

Gnomad4 FIN

AF:

0.409

Gnomad4 NFE

AF:

0.418

Gnomad4 OTH

AF:

0.385

Alfa

AF:

0.410

Hom.:

5019

Bravo

AF:

0.372

Asia WGS

AF:

0.214

AC:

746

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	Jun 18, 2018	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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Benign

0.90

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