Genetic Variant ENTPD1:c.16+432T>C (chr10-95756687-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001776.6(ENTPD1):c.16+432T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0556 in 168,922 control chromosomes in the GnomAD database, including 507 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.057 ( 461 hom., cov: 31)

Exomes 𝑓: 0.045 ( 46 hom. )

Consequence

ENTPD1
NM_001776.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.93

Publications

2 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.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD1	NM_001776.6 link	c.16+432T>C		intron_variant	Intron 1 of 9	ENST00000371205.5	NP_001767.3	P49961-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000371205.5 link	c.16+432T>C		intron_variant	Intron 1 of 9	1	NM_001776.6	ENSP00000360248.4		P49961-1

Frequencies

GnomAD3 genomes

AF:

0.0567

AC:

8617

AN:

152106

Hom.:

459

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0618

Gnomad ASJ

AF:

0.00518

Gnomad EAS

AF:

0.164

Gnomad SAS

AF:

0.136

Gnomad FIN

AF:

0.0609

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00914

Gnomad OTH

AF:

0.0427

GnomAD4 exome

AF:

0.0448

AC:

748

AN:

16698

Hom.:

Cov.:

AF XY:

0.0497

AC XY:

463

AN XY:

9322

show subpopulations

African (AFR)

AF:

0.124

AC:

AN:

266

American (AMR)

AF:

0.0756

AC:

144

AN:

1904

Ashkenazi Jewish (ASJ)

AF:

0.00345

AC:

AN:

290

East Asian (EAS)

AF:

0.169

AC:

142

AN:

842

South Asian (SAS)

AF:

0.123

AC:

304

AN:

2474

European-Finnish (FIN)

AF:

0.0266

AC:

AN:

376

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00989

AC:

AN:

9804

Other (OTH)

AF:

0.0238

AC:

AN:

714

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

101

135

169

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.0567

AC:

8637

AN:

152224

Hom.:

461

Cov.:

AF XY:

0.0609

AC XY:

4531

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.115

AC:

4793

AN:

41510

American (AMR)

AF:

0.0622

AC:

952

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.00518

AC:

AN:

3472

East Asian (EAS)

AF:

0.164

AC:

847

AN:

5178

South Asian (SAS)

AF:

0.135

AC:

654

AN:

4832

European-Finnish (FIN)

AF:

0.0609

AC:

645

AN:

10596

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00916

AC:

623

AN:

68022

Other (OTH)

AF:

0.0451

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

403

806

1210

1613

2016

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

106

212

318

424

530

<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:

0.0284

Hom.:

Bravo

AF:

0.0581

Asia WGS

AF:

0.162

AC:

563

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.40

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

1.9

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over