rs138292988
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PS1_ModerateBP4_StrongBP6_Very_StrongBS2
The NM_001039569.2(AP1S3):c.97C>T(p.Arg33Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00961 in 1,614,002 control chromosomes in the GnomAD database, including 112 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_001039569.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP1S3 | NM_001039569.2 | c.97C>T | p.Arg33Trp | missense_variant | 2/5 | ENST00000396654.7 | |
AP1S3 | XM_011510600.4 | c.97C>T | p.Arg33Trp | missense_variant | 2/4 | ||
AP1S3 | NR_110905.2 | n.229C>T | non_coding_transcript_exon_variant | 2/6 | |||
AP1S3 | NR_110906.2 | n.229C>T | non_coding_transcript_exon_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP1S3 | ENST00000396654.7 | c.97C>T | p.Arg33Trp | missense_variant | 2/5 | 2 | NM_001039569.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00719 AC: 1093AN: 152118Hom.: 10 Cov.: 33
GnomAD3 exomes AF: 0.00760 AC: 1896AN: 249412Hom.: 9 AF XY: 0.00771 AC XY: 1043AN XY: 135318
GnomAD4 exome AF: 0.00986 AC: 14417AN: 1461766Hom.: 102 Cov.: 31 AF XY: 0.00972 AC XY: 7067AN XY: 727170
GnomAD4 genome ? AF: 0.00718 AC: 1093AN: 152236Hom.: 10 Cov.: 33 AF XY: 0.00688 AC XY: 512AN XY: 74432
ClinVar
Submissions by phenotype
Psoriasis 15, pustular, susceptibility to Benign:1Other:1
risk factor, no assertion criteria provided | literature only | OMIM | May 01, 2014 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 20, 2022 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF 1.2%. Limited evidence for gene-disease association. - |
AP1S3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 02, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | AP1S3: BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at