Variant chr3-40416033-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001248.4(ENTPD3):c.791G>A(p.Arg264Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00492 in 1,613,954 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0038 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0050 ( 33 hom. )

Consequence

ENTPD3
NM_001248.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.92

Variant links:

Genes affected

ENTPD3 (HGNC:3365): (ectonucleoside triphosphate diphosphohydrolase 3) This gene encodes a plasma membrane-bound divalent cation-dependent E-type nucleotidase. The encoded protein is involved in the regulation of extracellular levels of ATP by hydrolysis of it and other nucleotides. Multiple transcript variants have been described. [provided by RefSeq, May 2014]

ENTPD3 links:

ENTPD3-AS1 (HGNC:):

ENTPD3-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.01149714).

BP6

Variant 3-40416033-G-A is Benign according to our data. Variant chr3-40416033-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2653692.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTPD3	NM_001248.4 linkuse as main transcript	c.791G>A	p.Arg264Gln	missense_variant	7/11	ENST00000301825.8	NP_001239.2	O75355-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTPD3	ENST00000301825.8 linkuse as main transcript	c.791G>A	p.Arg264Gln	missense_variant	7/11	1	NM_001248.4	ENSP00000301825.3		O75355-1

Frequencies

GnomAD3 genomes

AF:

0.00384

AC:

584

AN:

152122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000942

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00432

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00415

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00612

Gnomad OTH

AF:

0.00768

GnomAD3 exomes

AF:

0.00348

AC:

873

AN:

250774

Hom.:

AF XY:

0.00351

AC XY:

475

AN XY:

135504

show subpopulations

Gnomad AFR exome

AF:

0.00111

Gnomad AMR exome

AF:

0.00359

Gnomad ASJ exome

AF:

0.000398

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.00393

Gnomad NFE exome

AF:

0.00542

Gnomad OTH exome

AF:

0.00442

GnomAD4 exome

AF:

0.00503

AC:

7351

AN:

1461714

Hom.:

Cov.:

AF XY:

0.00490

AC XY:

3564

AN XY:

727146

show subpopulations

Gnomad4 AFR exome

AF:

0.000747

Gnomad4 AMR exome

AF:

0.00382

Gnomad4 ASJ exome

AF:

0.000612

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000812

Gnomad4 FIN exome

AF:

0.00472

Gnomad4 NFE exome

AF:

0.00596

Gnomad4 OTH exome

AF:

0.00414

GnomAD4 genome

AF:

0.00384

AC:

584

AN:

152240

Hom.:

Cov.:

AF XY:

0.00360

AC XY:

268

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.000939

Gnomad4 AMR

AF:

0.00431

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000208

Gnomad4 FIN

AF:

0.00415

Gnomad4 NFE

AF:

0.00612

Gnomad4 OTH

AF:

0.00760

Alfa

AF:

0.00481

Hom.:

Bravo

AF:

0.00396

TwinsUK

AF:

0.00701

AC:

ALSPAC

AF:

0.00675

AC:

ESP6500AA

AF:

0.00204

AC:

ESP6500EA

AF:

0.00663

AC:

ExAC

AF:

0.00344

AC:

418

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00638

EpiControl

AF:

0.00581

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

ENTPD3: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.038

T;T;.

Eigen

Benign

-0.14

Eigen_PC

Benign

-0.022

FATHMM_MKL

Uncertain

0.84

LIST_S2

Uncertain

0.88

.;D;D

M_CAP

Benign

0.0076

MetaRNN

Benign

0.011

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.3

L;L;L

PrimateAI

Benign

0.28

PROVEAN

Benign

-1.3

N;N;N

REVEL

Benign

0.052

Sift

Benign

0.25

T;T;T

Sift4G

Benign

0.38

T;T;T

Polyphen

0.31

B;B;.

Vest4

0.40

MVP

0.32

MPC

0.088

ClinPred

0.023

GERP RS

3.5

Varity_R

0.15

gMVP

0.50

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