rs3181123
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001776.6(ENTPD1):c.814-128C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 1,081,116 control chromosomes in the GnomAD database, including 22,517 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.23 ( 4591 hom., cov: 32)
Exomes 𝑓: 0.19 ( 17926 hom. )
Consequence
ENTPD1
NM_001776.6 intron
NM_001776.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.741
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 10-95847318-C-T is Benign according to our data. Variant chr10-95847318-C-T is described in ClinVar as [Benign]. Clinvar id is 1293400.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENTPD1 | NM_001776.6 | c.814-128C>T | intron_variant | ENST00000371205.5 | |||
ENTPD1-AS1 | NR_038444.1 | n.533+74G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENTPD1 | ENST00000371205.5 | c.814-128C>T | intron_variant | 1 | NM_001776.6 | P1 | |||
ENST00000433113.1 | n.260+13551C>T | intron_variant, non_coding_transcript_variant | 2 | ||||||
ENTPD1-AS1 | ENST00000669711.1 | n.443+29200G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.227 AC: 34554AN: 151942Hom.: 4578 Cov.: 32
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GnomAD4 exome AF: 0.186 AC: 172817AN: 929056Hom.: 17926 AF XY: 0.190 AC XY: 91725AN XY: 483296
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GnomAD4 genome ? AF: 0.228 AC: 34626AN: 152060Hom.: 4591 Cov.: 32 AF XY: 0.232 AC XY: 17223AN XY: 74332
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at