chr12-98665549-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_181861.2(APAF1):c.956-4A>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000392 in 1,329,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_181861.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APAF1 | NM_181861.2 | c.956-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000551964.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APAF1 | ENST00000551964.6 | c.956-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_181861.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 151102Hom.: 0 Cov.: 31 FAILED QC
GnomAD3 exomes AF: 0.0000205 AC: 5AN: 243938Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132502
GnomAD4 exome AF: 0.000392 AC: 521AN: 1329970Hom.: 0 Cov.: 29 AF XY: 0.000351 AC XY: 234AN XY: 666434
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151102Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73760
ClinVar
Submissions by phenotype
APAF1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 21, 2019 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at