GeneBe

rs201751093

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 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
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 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
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000131
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-74444090; API