Variant 10-95711826-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001098175.2(ENTPD1):c.-131T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0133 in 1,320,992 control chromosomes in the GnomAD database, including 179 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 18 hom., cov: 32)

Exomes 𝑓: 0.014 ( 161 hom. )

Consequence

ENTPD1
NM_001098175.2 5_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.238

Variant links:

Genes affected

ENTPD1 (HGNC:3363): (ectonucleoside triphosphate diphosphohydrolase 1) The protein encoded by this gene is a plasma membrane protein that hydrolyzes extracellular ATP and ADP to AMP. Inhibition of this protein's activity may confer anticancer benefits. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015]

ENTPD1 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=-0.73).

BP6

Variant 10-95711826-T-C is Benign according to our data. Variant chr10-95711826-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1300977.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0114 (1735/152328) while in subpopulation NFE AF= 0.0136 (926/68024). AF 95% confidence interval is 0.0129. There are 18 homozygotes in gnomad4. There are 949 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 18 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	Protein	UniProt
ENTPD1	NM_001098175.2 link	c.-131T>C	5_prime_UTR_variant	1/10	NP_001091645.1	P49961-2
ENTPD1	XM_011540371.3 link	c.-108-23T>C	intron_variant		XP_011538673.1	P49961-2
ENTPD1	XM_047426023.1 link	c.-108-23T>C	intron_variant		XP_047281979.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000453258 link	c.-131T>C		5_prime_UTR_variant	1/10	1		ENSP00000390955.2		P49961-2

Frequencies

GnomAD3 genomes

AF:

0.0114

AC:

1734

AN:

152210

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00227

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.00838

Gnomad ASJ

AF:

0.00864

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0124

Gnomad FIN

AF:

0.0417

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0136

Gnomad OTH

AF:

0.0119

GnomAD4 exome

AF:

0.0135

AC:

15798

AN:

1168664

Hom.:

161

Cov.:

AF XY:

0.0133

AC XY:

7877

AN XY:

594176

show subpopulations

Gnomad4 AFR exome

AF:

0.00184

Gnomad4 AMR exome

AF:

0.00619

Gnomad4 ASJ exome

AF:

0.00614

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00775

Gnomad4 FIN exome

AF:

0.0386

Gnomad4 NFE exome

AF:

0.0143

Gnomad4 OTH exome

AF:

0.0106

GnomAD4 genome

AF:

0.0114

AC:

1735

AN:

152328

Hom.:

Cov.:

AF XY:

0.0127

AC XY:

949

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.00226

Gnomad4 AMR

AF:

0.00836

Gnomad4 ASJ

AF:

0.00864

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0124

Gnomad4 FIN

AF:

0.0417

Gnomad4 NFE

AF:

0.0136

Gnomad4 OTH

AF:

0.0118

Alfa

AF:

0.0114

Hom.:

Bravo

AF:

0.00858

Asia WGS

AF:

0.00289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 09, 2021	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

4.8

DANN

Benign

0.57

Splicing

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