10-99704483-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020354.5(ENTPD7):c.1615C>T(p.His539Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,614,122 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020354.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENTPD7 | ENST00000370489.5 | c.1615C>T | p.His539Tyr | missense_variant | Exon 13 of 13 | 1 | NM_020354.5 | ENSP00000359520.4 | ||
ENSG00000285932 | ENST00000649102.1 | n.*460+11865G>A | intron_variant | Intron 8 of 12 | ENSP00000497114.1 | |||||
CUTC | ENST00000493385.5 | n.116+1810C>T | intron_variant | Intron 1 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251436Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135888
GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 727244
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1615C>T (p.H539Y) alteration is located in exon 13 (coding exon 12) of the ENTPD7 gene. This alteration results from a C to T substitution at nucleotide position 1615, causing the histidine (H) at amino acid position 539 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at