Genetic Variant ENTPD6:c.*841T>C (chr20-25226438-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001247.5(ENTPD6):c.*841T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 152,492 control chromosomes in the GnomAD database, including 22,204 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 0.52 ( 22153 hom., cov: 32)

Exomes 𝑓: 0.45 ( 51 hom. )

Consequence

ENTPD6
NM_001247.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.251

Publications

33 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:

ENSG00000279322 (HGNC:):

ENSG00000279322 links:

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new If you want to explore the variant's impact on the transcript NM_001247.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 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	UniProt
ENTPD6	NM_001247.5	MANE Select	c.*841T>C	3_prime_UTR	Exon 15 of 15	NP_001238.3	O75354-1
ENTPD6	NM_001322378.2		c.*841T>C	3_prime_UTR	Exon 15 of 15	NP_001309307.2	O75354-1
ENTPD6	NM_001317941.3		c.*841T>C	3_prime_UTR	Exon 15 of 15	NP_001304870.2	O75354-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENTPD6	ENST00000376652.9	TSL:1 MANE Select	c.*841T>C	3_prime_UTR	Exon 15 of 15	ENSP00000365840.4	O75354-1
ENTPD6	ENST00000360031.6	TSL:1	c.*841T>C	3_prime_UTR	Exon 15 of 15	ENSP00000353131.2	O75354-3
ENTPD6	ENST00000354989.10	TSL:1	c.*841T>C	3_prime_UTR	Exon 14 of 14	ENSP00000347084.6

Frequencies

GnomAD3 genomes

AF:

0.524

AC:

79541

AN:

151890

Hom.:

22125

Cov.:

show subpopulations

Gnomad AFR

AF:

0.672

Gnomad AMI

AF:

0.504

Gnomad AMR

AF:

0.411

Gnomad ASJ

AF:

0.322

Gnomad EAS

AF:

0.921

Gnomad SAS

AF:

0.468

Gnomad FIN

AF:

0.473

Gnomad MID

AF:

0.418

Gnomad NFE

AF:

0.452

Gnomad OTH

AF:

0.486

GnomAD4 exome

AF:

0.450

AC:

218

AN:

484

Hom.:

Cov.:

AF XY:

0.486

AC XY:

141

AN XY:

290

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.444

AC:

191

AN:

430

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.425

AC:

AN:

Other (OTH)

AF:

0.667

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.524

AC:

79611

AN:

152008

Hom.:

22153

Cov.:

AF XY:

0.523

AC XY:

38854

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.673

AC:

27894

AN:

41472

American (AMR)

AF:

0.410

AC:

6263

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.322

AC:

1117

AN:

3466

East Asian (EAS)

AF:

0.921

AC:

4750

AN:

5156

South Asian (SAS)

AF:

0.467

AC:

2249

AN:

4818

European-Finnish (FIN)

AF:

0.473

AC:

4990

AN:

10550

Middle Eastern (MID)

AF:

0.422

AC:

124

AN:

294

European-Non Finnish (NFE)

AF:

0.452

AC:

30734

AN:

67962

Other (OTH)

AF:

0.488

AC:

1030

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1877

3753

5630

7506

9383

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

690

1380

2070

2760

3450

<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:

0.470

Hom.:

48914

Bravo

AF:

0.525

Asia WGS

AF:

0.691

AC:

2400

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

5.8

(source)

DANN

Benign

0.74

PhyloP100

-0.25

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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