Genetic Variant ENTPD5:c.442-15_442-14dupTT (chr14-73977387-G-GAA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001249.5(ENTPD5):c.442-15_442-14dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00047 ( 0 hom., cov: 0)

Exomes 𝑓: 0.018 ( 0 hom. )

Consequence

ENTPD5
NM_001249.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.242

Publications

0 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:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001249.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENTPD5	NM_001249.5	MANE Select	c.442-15_442-14dupTT	intron	N/A	NP_001240.1	O75356
ENTPD5	NM_001321985.3		c.442-15_442-14dupTT	intron	N/A	NP_001308914.1	O75356
ENTPD5	NM_001321986.3		c.442-15_442-14dupTT	intron	N/A	NP_001308915.1	O75356

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENTPD5	ENST00000334696.11	TSL:5 MANE Select	c.442-14_442-13insTT	intron	N/A	ENSP00000335246.6	O75356
ENTPD5	ENST00000900912.1		c.466-14_466-13insTT	intron	N/A	ENSP00000570971.1
ENTPD5	ENST00000900901.1		c.442-14_442-13insTT	intron	N/A	ENSP00000570960.1

Frequencies

GnomAD3 genomes

AF:

0.000466

AC:

AN:

122278

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000226

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000655

Gnomad ASJ

AF:

0.00162

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000303

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000555

Gnomad OTH

AF:

0.00121

GnomAD2 exomes

AF:

0.0102

AC:

1469

AN:

143370

AF XY:

0.0101

show subpopulations

Gnomad AFR exome

AF:

0.00329

Gnomad AMR exome

AF:

0.0119

Gnomad ASJ exome

AF:

0.0145

Gnomad EAS exome

AF:

0.00163

Gnomad FIN exome

AF:

0.0109

Gnomad NFE exome

AF:

0.0119

Gnomad OTH exome

AF:

0.0142

GnomAD4 exome

AF:

0.0178

AC:

18233

AN:

1022944

Hom.:

Cov.:

AF XY:

0.0169

AC XY:

8837

AN XY:

522750

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00464

AC:

105

AN:

22624

American (AMR)

AF:

0.0117

AC:

359

AN:

30660

Ashkenazi Jewish (ASJ)

AF:

0.0161

AC:

336

AN:

20846

East Asian (EAS)

AF:

0.00187

AC:

AN:

34682

South Asian (SAS)

AF:

0.00803

AC:

549

AN:

68362

European-Finnish (FIN)

AF:

0.0144

AC:

567

AN:

39294

Middle Eastern (MID)

AF:

0.00925

AC:

AN:

4434

European-Non Finnish (NFE)

AF:

0.0205

AC:

15523

AN:

757716

Other (OTH)

AF:

0.0155

AC:

688

AN:

44326

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.296

Heterozygous variant carriers

1506

3012

4517

6023

7529

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

574

1148

1722

2296

2870

<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:

0.000466

AC:

AN:

122300

Hom.:

Cov.:

AF XY:

0.000615

AC XY:

AN XY:

58536

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000225

AC:

AN:

31070

American (AMR)

AF:

0.000654

AC:

AN:

12228

Ashkenazi Jewish (ASJ)

AF:

0.00162

AC:

AN:

3082

East Asian (EAS)

AF:

0.00

AC:

AN:

3552

South Asian (SAS)

AF:

0.00

AC:

AN:

3634

European-Finnish (FIN)

AF:

0.000303

AC:

AN:

6608

Middle Eastern (MID)

AF:

0.00

AC:

AN:

240

European-Non Finnish (NFE)

AF:

0.000555

AC:

AN:

59440

Other (OTH)

AF:

0.00120

AC:

AN:

1660

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.0000000000218325), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.386

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.24

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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14-73977387-GAAAAAA-GAAAAAAAA

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