rs2226163
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001776.6(ENTPD1):c.*2854A>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 0.00000766 in 130,584 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000077 ( 0 hom., cov: 21)
Consequence
ENTPD1
NM_001776.6 3_prime_UTR
NM_001776.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.700
Genes affected
ENTPD1 (HGNC:3363): (ectonucleoside triphosphate diphosphohydrolase 1) The protein encoded by this gene is a plasma membrane protein that hydrolyzes extracellular ATP and ADP to AMP. Inhibition of this protein's activity may confer anticancer benefits. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENTPD1 | NM_001776.6 | c.*2854A>C | 3_prime_UTR_variant | 10/10 | ENST00000371205.5 | ||
ENTPD1-AS1 | NR_038444.1 | n.439+7281T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENTPD1 | ENST00000371205.5 | c.*2854A>C | 3_prime_UTR_variant | 10/10 | 1 | NM_001776.6 | P1 | ||
ENST00000433113.1 | n.261-4195A>C | intron_variant, non_coding_transcript_variant | 2 | ||||||
ENTPD1-AS1 | ENST00000669711.1 | n.443+7281T>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000766 AC: 1AN: 130584Hom.: 0 Cov.: 21
GnomAD3 genomes
?
AF:
AC:
1
AN:
130584
Hom.:
Cov.:
21
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Cov.: 8
GnomAD4 exome
Cov.:
8
GnomAD4 genome ? AF: 0.00000766 AC: 1AN: 130584Hom.: 0 Cov.: 21 AF XY: 0.0000161 AC XY: 1AN XY: 61982
GnomAD4 genome
?
AF:
AC:
1
AN:
130584
Hom.:
Cov.:
21
AF XY:
AC XY:
1
AN XY:
61982
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at