chr2-223777862-A-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 3P and 8B. PS1_ModeratePP3BP4_StrongBS2
The NM_001039569.2(AP1S3):āc.11T>Gā(p.Phe4Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 1,613,370 control chromosomes in the GnomAD database, including 127 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). 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
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP1S3 | NM_001039569.2 | c.11T>G | p.Phe4Cys | missense_variant | 2/5 | ENST00000396654.7 | |
AP1S3 | XM_011510600.4 | c.11T>G | p.Phe4Cys | missense_variant | 2/4 | ||
AP1S3 | NR_110905.2 | n.143T>G | non_coding_transcript_exon_variant | 2/6 | |||
AP1S3 | NR_110906.2 | n.143T>G | non_coding_transcript_exon_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP1S3 | ENST00000396654.7 | c.11T>G | p.Phe4Cys | missense_variant | 2/5 | 2 | NM_001039569.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00865 AC: 1316AN: 152188Hom.: 13 Cov.: 33
GnomAD3 exomes AF: 0.00759 AC: 1885AN: 248296Hom.: 19 AF XY: 0.00743 AC XY: 1001AN XY: 134682
GnomAD4 exome AF: 0.0111 AC: 16188AN: 1461064Hom.: 114 Cov.: 31 AF XY: 0.0109 AC XY: 7940AN XY: 726760
GnomAD4 genome AF: 0.00864 AC: 1316AN: 152306Hom.: 13 Cov.: 33 AF XY: 0.00822 AC XY: 612AN XY: 74486
ClinVar
Submissions by phenotype
AP1S3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 11, 2022 | 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: PP3, BS1, BS2 - |
Psoriasis 15, pustular, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | May 01, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at