chr12-98666331-A-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_181861.2(APAF1):c.1336A>T(p.Thr446Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00242 in 1,613,254 control chromosomes in the GnomAD database, including 83 homozygotes. 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 Benign (★★).
Frequency
Consequence
NM_181861.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APAF1 | NM_181861.2 | c.1336A>T | p.Thr446Ser | missense_variant | 9/27 | ENST00000551964.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APAF1 | ENST00000551964.6 | c.1336A>T | p.Thr446Ser | missense_variant | 9/27 | 1 | NM_181861.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0129 AC: 1956AN: 152168Hom.: 37 Cov.: 32
GnomAD3 exomes AF: 0.00344 AC: 862AN: 250606Hom.: 17 AF XY: 0.00253 AC XY: 342AN XY: 135394
GnomAD4 exome AF: 0.00134 AC: 1955AN: 1460970Hom.: 46 Cov.: 32 AF XY: 0.00112 AC XY: 816AN XY: 726688
GnomAD4 genome AF: 0.0129 AC: 1957AN: 152284Hom.: 37 Cov.: 32 AF XY: 0.0123 AC XY: 919AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
APAF1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at