rs201997946
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_031307.4(PUS3):c.1361A>T(p.Asn454Ile) 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. 15/21 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. N454S) has been classified as Uncertain significance.
Frequency
Consequence
NM_031307.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PUS3 | NM_031307.4 | c.1361A>T | p.Asn454Ile | missense_variant | Exon 4 of 4 | ENST00000227474.8 | NP_112597.4 | |
HYLS1 | NM_001134793.2 | c.-26+2398T>A | intron_variant | Intron 2 of 2 | ENST00000425380.7 | NP_001128265.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PUS3 | ENST00000227474.8 | c.1361A>T | p.Asn454Ile | missense_variant | Exon 4 of 4 | 1 | NM_031307.4 | ENSP00000227474.3 | ||
HYLS1 | ENST00000425380.7 | c.-26+2398T>A | intron_variant | Intron 2 of 2 | 3 | NM_001134793.2 | ENSP00000414884.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at