Genetic Variant ENTPD1:c.16+273delT (chr10-95756521-GT-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001776.6(ENTPD1):c.16+273delT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.54 ( 22521 hom., cov: 0)

Exomes 𝑓: 0.52 ( 44515 hom. )

Consequence

ENTPD1
NM_001776.6 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.335

Publications

0 publications found

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:

ENTPD1-AS1 (HGNC:45203): (ENTPD1 antisense RNA 1)

ENTPD1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 10-95756521-GT-G is Benign according to our data. Variant chr10-95756521-GT-G is described in ClinVar as Benign. ClinVar VariationId is 1274919.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001776.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENTPD1	NM_001776.6	MANE Select	c.16+273delT	intron	N/A	NP_001767.3
ENTPD1	NM_001164178.1		c.52+762delT	intron	N/A	NP_001157650.1	P49961-6
ENTPD1	NM_001098175.2		c.37+44535delT	intron	N/A	NP_001091645.1	P49961-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENTPD1	ENST00000371205.5	TSL:1 MANE Select	c.16+273delT	intron	N/A	ENSP00000360248.4	P49961-1
ENTPD1	ENST00000453258.6	TSL:1	c.37+44535delT	intron	N/A	ENSP00000390955.2	P49961-2
ENTPD1	ENST00000635076.1	TSL:1	n.16+273delT	intron	N/A	ENSP00000489250.1	A0A0U1RQZ5

Frequencies

GnomAD3 genomes

AF:

0.539

AC:

81814

AN:

151650

Hom.:

22505

Cov.:

show subpopulations

Gnomad AFR

AF:

0.545

Gnomad AMI

AF:

0.620

Gnomad AMR

AF:

0.627

Gnomad ASJ

AF:

0.386

Gnomad EAS

AF:

0.262

Gnomad SAS

AF:

0.565

Gnomad FIN

AF:

0.557

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.542

Gnomad OTH

AF:

0.504

GnomAD4 exome

AF:

0.517

AC:

164155

AN:

317616

Hom.:

44515

Cov.:

AF XY:

0.517

AC XY:

86607

AN XY:

167476

show subpopulations

African (AFR)

AF:

0.542

AC:

5156

AN:

9516

American (AMR)

AF:

0.653

AC:

8020

AN:

12284

Ashkenazi Jewish (ASJ)

AF:

0.379

AC:

3833

AN:

10106

East Asian (EAS)

AF:

0.306

AC:

6903

AN:

22544

South Asian (SAS)

AF:

0.552

AC:

16601

AN:

30076

European-Finnish (FIN)

AF:

0.527

AC:

9331

AN:

17690

Middle Eastern (MID)

AF:

0.404

AC:

655

AN:

1622

European-Non Finnish (NFE)

AF:

0.534

AC:

104171

AN:

195096

Other (OTH)

AF:

0.508

AC:

9485

AN:

18682

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

3574

7148

10721

14295

17869

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

516

1032

1548

2064

2580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.539

AC:

81877

AN:

151768

Hom.:

22521

Cov.:

AF XY:

0.542

AC XY:

40165

AN XY:

74136

show subpopulations

African (AFR)

AF:

0.545

AC:

22554

AN:

41354

American (AMR)

AF:

0.626

AC:

9555

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.386

AC:

1335

AN:

3460

East Asian (EAS)

AF:

0.262

AC:

1347

AN:

5142

South Asian (SAS)

AF:

0.563

AC:

2708

AN:

4814

European-Finnish (FIN)

AF:

0.557

AC:

5854

AN:

10504

Middle Eastern (MID)

AF:

0.384

AC:

113

AN:

294

European-Non Finnish (NFE)

AF:

0.542

AC:

36788

AN:

67926

Other (OTH)

AF:

0.501

AC:

1060

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1859

3719

5578

7438

9297

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

702

1404

2106

2808

3510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.432

Hom.:

1247

Bravo

AF:

0.543

Asia WGS

AF:

0.438

AC:

1527

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.34

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over