chr20-3823890-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018347.3(AP5S1):c.196C>T(p.Arg66Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000287 in 1,600,938 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018347.3 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 |
---|---|---|---|---|---|---|---|
AP5S1 | NM_018347.3 | c.196C>T | p.Arg66Trp | missense_variant | 3/3 | ENST00000615891.2 | |
AP5S1 | NM_001204446.2 | c.196C>T | p.Arg66Trp | missense_variant | 3/3 | ||
AP5S1 | NM_001204447.2 | c.196C>T | p.Arg66Trp | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP5S1 | ENST00000615891.2 | c.196C>T | p.Arg66Trp | missense_variant | 3/3 | 1 | NM_018347.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000374 AC: 9AN: 240456Hom.: 0 AF XY: 0.0000229 AC XY: 3AN XY: 131072
GnomAD4 exome AF: 0.0000262 AC: 38AN: 1448730Hom.: 0 Cov.: 32 AF XY: 0.0000208 AC XY: 15AN XY: 720798
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74374
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at