Genetic Variant ENTPD5:c.442-16_442-14dupTTT (chr14-73977387-G-GAAA) – 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.442-16_442-14dupTTT 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 0.000041 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00032 ( 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.442-16_442-14dupTTT	intron	N/A	NP_001240.1	O75356
ENTPD5	NM_001321985.3		c.442-16_442-14dupTTT	intron	N/A	NP_001308914.1	O75356
ENTPD5	NM_001321986.3		c.442-16_442-14dupTTT	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_442-13insTTT	intron	N/A	ENSP00000335246.6	O75356
ENTPD5	ENST00000900912.1		c.466-14_466-13insTTT	intron	N/A	ENSP00000570971.1
ENTPD5	ENST00000900901.1		c.442-14_442-13insTTT	intron	N/A	ENSP00000570960.1

Frequencies

GnomAD3 genomes

AF:

0.0000409

AC:

AN:

122288

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000303

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000505

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000322

AC:

332

AN:

1029896

Hom.:

Cov.:

AF XY:

0.000277

AC XY:

146

AN XY:

526250

show subpopulations

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

African (AFR)

AF:

0.0000879

AC:

AN:

22742

American (AMR)

AF:

0.0000973

AC:

AN:

30844

Ashkenazi Jewish (ASJ)

AF:

0.000238

AC:

AN:

21018

East Asian (EAS)

AF:

0.00

AC:

AN:

34816

South Asian (SAS)

AF:

0.000116

AC:

AN:

68790

European-Finnish (FIN)

AF:

0.000177

AC:

AN:

39618

Middle Eastern (MID)

AF:

0.000225

AC:

AN:

4452

European-Non Finnish (NFE)

AF:

0.000381

AC:

291

AN:

763020

Other (OTH)

AF:

0.000336

AC:

AN:

44596

⚠️ 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: 0.260

Heterozygous variant carriers

117

156

195

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.0000409

AC:

AN:

122288

Hom.:

Cov.:

AF XY:

0.0000171

AC XY:

AN XY:

58510

show subpopulations

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

African (AFR)

AF:

0.00

AC:

AN:

31018

American (AMR)

AF:

0.00

AC:

AN:

12208

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3084

East Asian (EAS)

AF:

0.00

AC:

AN:

3562

South Asian (SAS)

AF:

0.00

AC:

AN:

3656

European-Finnish (FIN)

AF:

0.000303

AC:

AN:

6608

Middle Eastern (MID)

AF:

0.00

AC:

AN:

262

European-Non Finnish (NFE)

AF:

0.0000505

AC:

AN:

59454

Other (OTH)

AF:

0.00

AC:

AN:

1650

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000000223952), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.315

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

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-GAAAAAAAAA

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