chr15-89903810-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_182616.4(ARPIN):c.475C>T(p.Arg159Trp) variant causes a missense change. The variant allele was found at a frequency of 0.000103 in 1,614,146 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R159Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_182616.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARPIN | NM_182616.4 | c.475C>T | p.Arg159Trp | missense_variant | 4/6 | ENST00000357484.10 | |
ARPIN-AP3S2 | NM_001199058.2 | c.475C>T | p.Arg159Trp | missense_variant | 4/10 | ||
ARPIN | NM_001282380.2 | c.187C>T | p.Arg63Trp | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARPIN | ENST00000357484.10 | c.475C>T | p.Arg159Trp | missense_variant | 4/6 | 1 | NM_182616.4 | P1 | |
ARPIN | ENST00000560096.1 | c.136C>T | p.Arg46Trp | missense_variant | 1/2 | 2 | |||
ARPIN | ENST00000460685.1 | c.187C>T | p.Arg63Trp | missense_variant | 4/6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000116 AC: 29AN: 249504Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135382
GnomAD4 exome AF: 0.0000910 AC: 133AN: 1461830Hom.: 0 Cov.: 32 AF XY: 0.000106 AC XY: 77AN XY: 727230
GnomAD4 genome AF: 0.000217 AC: 33AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74488
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at