Variant chr3-186079931-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP5BP4

The NM_004454.3(ETV5):c.536A>C(p.His179Pro) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Genomes: 𝑓 0.0096 ( 0 hom., cov: 0)

Exomes 𝑓: 0.017 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ETV5
NM_004454.3 missense

Scores

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 4.20

Variant links:

Genes affected

ETV5 (HGNC:3494): (ETS variant transcription factor 5) Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in cellular response to oxidative stress; negative regulation of transcription by RNA polymerase II; and positive regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ETV5 links:

ETV5-AS1 (HGNC:40222): (ETV5 antisense RNA 1)

ETV5-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PP5

Variant 3-186079931-T-G is Pathogenic according to our data. Variant chr3-186079931-T-G is described in ClinVar as [Pathogenic]. Clinvar id is 1801782.Status of the report is no_assertion_criteria_provided, 0 stars.

BP4

Computational evidence support a benign effect (MetaRNN=0.07760486). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ETV5	NM_004454.3 linkuse as main transcript	c.536A>C	p.His179Pro	missense_variant	7/13	ENST00000306376.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETV5	ENST00000306376.10 linkuse as main transcript	c.536A>C	p.His179Pro	missense_variant	7/13	1	NM_004454.3	P1	P41161-1
ETV5-AS1	ENST00000453370.1 linkuse as main transcript	n.172+590T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

136

AN:

14064

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00950

Gnomad AMI

AF:

0.0192

Gnomad AMR

AF:

0.00774

Gnomad ASJ

AF:

0.0107

Gnomad EAS

AF:

0.00643

Gnomad SAS

AF:

0.0121

Gnomad FIN

AF:

0.00542

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0104

Gnomad OTH

AF:

0.00877

GnomAD3 exomes

AF:

0.00143

AC:

225

AN:

157416

Hom.:

AF XY:

0.00143

AC XY:

126

AN XY:

88122

show subpopulations

Gnomad AFR exome

AF:

0.000578

Gnomad AMR exome

AF:

0.00159

Gnomad ASJ exome

AF:

0.00320

Gnomad EAS exome

AF:

0.000593

Gnomad SAS exome

AF:

0.00221

Gnomad FIN exome

AF:

0.00209

Gnomad NFE exome

AF:

0.00111

Gnomad OTH exome

AF:

0.00269

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0175

AC:

3570

AN:

204310

Hom.:

Cov.:

AF XY:

0.0184

AC XY:

2064

AN XY:

112290

show subpopulations

Gnomad4 AFR exome

AF:

0.0104

Gnomad4 AMR exome

AF:

0.00713

Gnomad4 ASJ exome

AF:

0.0171

Gnomad4 EAS exome

AF:

0.00468

Gnomad4 SAS exome

AF:

0.0341

Gnomad4 FIN exome

AF:

0.0103

Gnomad4 NFE exome

AF:

0.0172

Gnomad4 OTH exome

AF:

0.0236

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00964

AC:

136

AN:

14106

Hom.:

Cov.:

AF XY:

0.00941

AC XY:

AN XY:

7228

show subpopulations

Gnomad4 AFR

AF:

0.00943

Gnomad4 AMR

AF:

0.00769

Gnomad4 ASJ

AF:

0.0107

Gnomad4 EAS

AF:

0.00641

Gnomad4 SAS

AF:

0.0121

Gnomad4 FIN

AF:

0.00542

Gnomad4 NFE

AF:

0.0104

Gnomad4 OTH

AF:

0.00855

Alfa

AF:

0.0602

Hom.:

ExAC

AF:

0.000124

AC:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Myoepithelial tumor

Pathogenic:1

Pathogenic, no assertion criteria provided

research

Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine

Nov 01, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.059

BayesDel_addAF

Benign

-0.013

BayesDel_noAF

Benign

-0.26

CADD

Benign

DANN

Benign

0.93

DEOGEN2

Benign

0.095

T;T

Eigen

Benign

-0.080

Eigen_PC

Benign

0.010

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.46

.;T

M_CAP

Benign

0.0069

MetaRNN

Benign

0.078

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.34

N;N

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Uncertain

0.53

PROVEAN

Benign

-1.9

N;N

REVEL

Benign

0.11

Sift

Benign

0.049

D;D

Sift4G

Benign

0.16

T;T

Polyphen

0.0

B;B

Vest4

0.65

MutPred

0.40

Gain of glycosylation at H179 (P = 0.0037);Gain of glycosylation at H179 (P = 0.0037);

MVP

0.62

MPC

0.48

ClinPred

0.020

GERP RS

5.3

Varity_R

0.34

gMVP

0.33

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