chr10-99702592-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_020354.5(ENTPD7):c.1502G>A(p.Arg501Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,410 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_020354.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENTPD7 | ENST00000370489.5 | c.1502G>A | p.Arg501Gln | missense_variant | Exon 12 of 13 | 1 | NM_020354.5 | ENSP00000359520.4 | ||
ENSG00000285932 | ENST00000649102.1 | n.*461-10908C>T | intron_variant | Intron 8 of 12 | ENSP00000497114.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152070Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461340Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 726912
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152070Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74262
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at