Genetic Variant ENTPD6:c.1243+238C>G (chr20-25224395-C-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001247.5(ENTPD6):c.1243+238C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 378,204 control chromosomes in the GnomAD database, including 6,334 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 0.16 ( 2199 hom., cov: 33)

Exomes 𝑓: 0.18 ( 4135 hom. )

Consequence

ENTPD6
NM_001247.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.18

Publications

5 publications found

Variant links:

Genes affected

ENTPD6 (HGNC:3368): (ectonucleoside triphosphate diphosphohydrolase 6) ENTPD6 is similar to E-type nucleotidases (NTPases). NTPases, such as CD39, mediate catabolism of extracellular nucleotides. ENTPD6 contains 4 apyrase-conserved regions which are characteristic of NTPases. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

ENTPD6 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001247.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ENTPD6	NM_001247.5	MANE Select	c.1243+238C>G	intron	N/A	NP_001238.3
ENTPD6	NM_001322378.2		c.1243+238C>G	intron	N/A	NP_001309307.2
ENTPD6	NM_001317941.3		c.1240+238C>G	intron	N/A	NP_001304870.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ENTPD6	ENST00000376652.9	TSL:1 MANE Select	c.1243+238C>G	intron	N/A	ENSP00000365840.4
ENTPD6	ENST00000360031.6	TSL:1	c.1240+238C>G	intron	N/A	ENSP00000353131.2
ENTPD6	ENST00000354989.10	TSL:1	c.1159+238C>G	intron	N/A	ENSP00000347084.6

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

24158

AN:

152108

Hom.:

2195

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0782

Gnomad AMI

AF:

0.279

Gnomad AMR

AF:

0.164

Gnomad ASJ

AF:

0.0982

Gnomad EAS

AF:

0.328

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.193

Gnomad OTH

AF:

0.152

GnomAD4 exome

AF:

0.182

AC:

41181

AN:

225978

Hom.:

4135

Cov.:

AF XY:

0.179

AC XY:

21015

AN XY:

117170

show subpopulations

African (AFR)

AF:

0.0774

AC:

511

AN:

6602

American (AMR)

AF:

0.141

AC:

943

AN:

6688

Ashkenazi Jewish (ASJ)

AF:

0.0849

AC:

698

AN:

8224

East Asian (EAS)

AF:

0.318

AC:

5827

AN:

18300

South Asian (SAS)

AF:

0.122

AC:

1640

AN:

13472

European-Finnish (FIN)

AF:

0.190

AC:

3300

AN:

17352

Middle Eastern (MID)

AF:

0.0903

AC:

AN:

1096

European-Non Finnish (NFE)

AF:

0.183

AC:

25641

AN:

140100

Other (OTH)

AF:

0.178

AC:

2522

AN:

14144

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1595

3191

4786

6382

7977

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

132

264

396

528

660

<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:

0.159

AC:

24161

AN:

152226

Hom.:

2199

Cov.:

AF XY:

0.159

AC XY:

11844

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.0780

AC:

3240

AN:

41554

American (AMR)

AF:

0.164

AC:

2513

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0982

AC:

341

AN:

3472

East Asian (EAS)

AF:

0.329

AC:

1695

AN:

5156

South Asian (SAS)

AF:

0.124

AC:

597

AN:

4830

European-Finnish (FIN)

AF:

0.195

AC:

2069

AN:

10602

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.193

AC:

13099

AN:

67992

Other (OTH)

AF:

0.154

AC:

325

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1059

2119

3178

4238

5297

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

276

552

828

1104

1380

<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:

0.0985

Hom.:

183

Bravo

AF:

0.153

Asia WGS

AF:

0.255

AC:

883

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

(source)

DANN

Benign

0.73

PhyloP100

-1.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.23

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.23

Position offset: -8

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over