chr11-17089924-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_002645.4(PIK3C2A):c.4879-4G>A 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 0.0000215 in 1,532,330 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_002645.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3C2A | NM_002645.4 | c.4879-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000691414.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3C2A | ENST00000691414.1 | c.4879-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_002645.4 | P1 | ||||
PIK3C2A | ENST00000265970.11 | c.4879-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
PIK3C2A | ENST00000531428.1 | n.1400+1410G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 151958Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000387 AC: 8AN: 206874Hom.: 0 AF XY: 0.00000887 AC XY: 1AN XY: 112800
GnomAD4 exome AF: 0.0000181 AC: 25AN: 1380372Hom.: 0 Cov.: 27 AF XY: 0.0000176 AC XY: 12AN XY: 681088
GnomAD4 genome AF: 0.0000526 AC: 8AN: 151958Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74204
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at