rs200207416
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002526.4(NT5E):c.400G>A(p.Glu134Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E134Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_002526.4 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 |
---|---|---|---|---|---|---|---|---|---|---|
NT5E | ENST00000257770.8 | c.400G>A | p.Glu134Lys | missense_variant | Exon 2 of 9 | 1 | NM_002526.4 | ENSP00000257770.3 | ||
NT5E | ENST00000369646.7 | c.400G>A | p.Glu134Lys | missense_variant | Exon 2 of 3 | 1 | ENSP00000358660.3 | |||
NT5E | ENST00000369651.7 | c.400G>A | p.Glu134Lys | missense_variant | Exon 2 of 8 | 2 | ENSP00000358665.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at