dbSNP rs2074932: ENTPD5:p.Leu243Leu (chr14-73974981-G-A) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_001249.5(ENTPD5):c.727C>T(p.Leu243Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 1,608,022 control chromosomes in the GnomAD database, including 308,026 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 0.55 ( 24522 hom., cov: 31)

Exomes 𝑓: 0.62 ( 283504 hom. )

Consequence

ENTPD5
NM_001249.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.66

Publications

26 publications found

Variant links:

Genes affected

ENTPD5 (HGNC:3367): (ectonucleoside triphosphate diphosphohydrolase 5 (inactive)) The protein encoded by this gene is similar to E-type nucleotidases (NTPases)/ecto-ATPase/apyrases. NTPases, such as CD39, mediate catabolism of extracellular nucleotides. ENTPD5 contains 4 apyrase-conserved regions which is characteristic of NTPases. [provided by RefSeq, Jan 2009]

ENTPD5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP7

Synonymous conserved (PhyloP=1.66 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD5	NM_001249.5 link	c.727C>T	p.Leu243Leu	synonymous_variant	Exon 11 of 16	ENST00000334696.11	NP_001240.1	O75356A0A024R6D3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTPD5	ENST00000334696.11 link	c.727C>T	p.Leu243Leu	synonymous_variant	Exon 11 of 16	5	NM_001249.5	ENSP00000335246.6		O75356
ENTPD5	ENST00000557325.5 link	c.727C>T	p.Leu243Leu	synonymous_variant	Exon 11 of 16	2		ENSP00000451810.1		G3V4I0

Frequencies

GnomAD3 genomes

AF:

0.555

AC:

84256

AN:

151802

Hom.:

24521

Cov.:

show subpopulations

Gnomad AFR

AF:

0.397

Gnomad AMI

AF:

0.525

Gnomad AMR

AF:

0.647

Gnomad ASJ

AF:

0.630

Gnomad EAS

AF:

0.271

Gnomad SAS

AF:

0.611

Gnomad FIN

AF:

0.693

Gnomad MID

AF:

0.554

Gnomad NFE

AF:

0.623

Gnomad OTH

AF:

0.568

GnomAD2 exomes

AF:

0.600

AC:

150426

AN:

250886

AF XY:

0.603

show subpopulations

Gnomad AFR exome

AF:

0.393

Gnomad AMR exome

AF:

0.716

Gnomad ASJ exome

AF:

0.623

Gnomad EAS exome

AF:

0.244

Gnomad FIN exome

AF:

0.688

Gnomad NFE exome

AF:

0.626

Gnomad OTH exome

AF:

0.623

GnomAD4 exome

AF:

0.619

AC:

901209

AN:

1456102

Hom.:

283504

Cov.:

AF XY:

0.619

AC XY:

448592

AN XY:

724704

show subpopulations

African (AFR)

AF:

0.382

AC:

12755

AN:

33356

American (AMR)

AF:

0.707

AC:

31545

AN:

44618

Ashkenazi Jewish (ASJ)

AF:

0.629

AC:

16395

AN:

26076

East Asian (EAS)

AF:

0.299

AC:

11845

AN:

39662

South Asian (SAS)

AF:

0.619

AC:

53294

AN:

86048

European-Finnish (FIN)

AF:

0.689

AC:

36784

AN:

53392

Middle Eastern (MID)

AF:

0.578

AC:

3326

AN:

5754

European-Non Finnish (NFE)

AF:

0.631

AC:

698957

AN:

1106982

Other (OTH)

AF:

0.603

AC:

36308

AN:

60214

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

15161

30322

45484

60645

75806

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18392

36784

55176

73568

91960

<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:

0.555

AC:

84277

AN:

151920

Hom.:

24522

Cov.:

AF XY:

0.557

AC XY:

41358

AN XY:

74256

show subpopulations

African (AFR)

AF:

0.396

AC:

16415

AN:

41406

American (AMR)

AF:

0.647

AC:

9868

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.630

AC:

2187

AN:

3472

East Asian (EAS)

AF:

0.272

AC:

1406

AN:

5172

South Asian (SAS)

AF:

0.609

AC:

2936

AN:

4818

European-Finnish (FIN)

AF:

0.693

AC:

7311

AN:

10548

Middle Eastern (MID)

AF:

0.548

AC:

161

AN:

294

European-Non Finnish (NFE)

AF:

0.623

AC:

42320

AN:

67944

Other (OTH)

AF:

0.567

AC:

1196

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1789

3578

5368

7157

8946

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

728

1456

2184

2912

3640

<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:

0.603

Hom.:

88333

Bravo

AF:

0.544

Asia WGS

AF:

0.469

AC:

1634

AN:

3476

EpiCase

AF:

0.621

EpiControl

AF:

0.629

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

4.7

(source)

DANN

Benign

0.79

PhyloP100

1.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.7

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

Splicevardb

2.0

SpliceAI score (max)

0.040

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