6-85489525-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002526.4(NT5E):c.1136T>A(p.Met379Lys) 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. M379T) has been classified as Likely benign.
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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NT5E | NM_002526.4 | c.1136T>A | p.Met379Lys | missense_variant | 6/9 | ENST00000257770.8 | |
NT5E | NM_001204813.2 | c.1136T>A | p.Met379Lys | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5E | ENST00000257770.8 | c.1136T>A | p.Met379Lys | missense_variant | 6/9 | 1 | NM_002526.4 | P1 | |
NT5E | ENST00000369651.7 | c.1136T>A | p.Met379Lys | missense_variant | 6/8 | 2 | |||
NT5E | ENST00000416334.5 | c.431T>A | p.Met144Lys | missense_variant | 4/5 | 3 | |||
NT5E | ENST00000437581.1 | c.224T>A | p.Met75Lys | missense_variant | 3/5 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 35
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at