rs6773917
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001248.4(ENTPD3):c.*255G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 31)
Exomes 𝑓: 0.0000084 ( 0 hom. )
Consequence
ENTPD3
NM_001248.4 3_prime_UTR
NM_001248.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.686
Genes affected
ENTPD3 (HGNC:3365): (ectonucleoside triphosphate diphosphohydrolase 3) This gene encodes a plasma membrane-bound divalent cation-dependent E-type nucleotidase. The encoded protein is involved in the regulation of extracellular levels of ATP by hydrolysis of it and other nucleotides. Multiple transcript variants have been described. [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENTPD3 | NM_001248.4 | c.*255G>A | 3_prime_UTR_variant | 11/11 | ENST00000301825.8 | ||
ENTPD3-AS1 | NR_040100.1 | n.265+23942C>T | intron_variant, non_coding_transcript_variant | ||||
ENTPD3 | NM_001291960.2 | c.*255G>A | 3_prime_UTR_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENTPD3 | ENST00000301825.8 | c.*255G>A | 3_prime_UTR_variant | 11/11 | 1 | NM_001248.4 | P1 | ||
ENTPD3-AS1 | ENST00000439293.5 | n.143+23942C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
GnomAD4 exome AF: 0.00000837 AC: 3AN: 358352Hom.: 0 Cov.: 0 AF XY: 0.0000106 AC XY: 2AN XY: 187856
GnomAD4 exome
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3
AN:
358352
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0
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2
AN XY:
187856
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GnomAD4 genome ? Cov.: 31
GnomAD4 genome
?
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at