GeneBe

rs201751093

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001249.5(ENTPD5):​c.442-19_442-14delTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000097 in 1,030,624 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 9.7e-7 ( 0 hom. )

Consequence

ENTPD5
NM_001249.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.67

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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ENTPD5NM_001249.5 linkc.442-19_442-14delTTTTTT intron_variant Intron 6 of 15 ENST00000334696.11 NP_001240.1 O75356A0A024R6D3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENTPD5ENST00000334696.11 linkc.442-19_442-14delTTTTTT intron_variant Intron 6 of 15 5 NM_001249.5 ENSP00000335246.6 O75356
ENTPD5ENST00000557325.5 linkc.442-19_442-14delTTTTTT intron_variant Intron 6 of 15 2 ENSP00000451810.1 G3V4I0
ENTPD5ENST00000553284.5 linkc.442-19_442-14delTTTTTT intron_variant Intron 4 of 6 3 ENSP00000451591.1 G3V450

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
9.70e-7
AC:
1
AN:
1030624
Hom.:
0
AF XY:
0.00000190
AC XY:
1
AN XY:
526640
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
22748
American (AMR)
AF:
0.00
AC:
0
AN:
30854
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
21024
East Asian (EAS)
AF:
0.00
AC:
0
AN:
34824
South Asian (SAS)
AF:
0.00
AC:
0
AN:
68828
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
39632
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4452
European-Non Finnish (NFE)
AF:
0.00000131
AC:
1
AN:
763638
Other (OTH)
AF:
0.00
AC:
0
AN:
44624
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.7

Splicing

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

Publications

Other links and lift over

dbSNP: rs201751093; hg19: chr14-74444090; API