rs72561481
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP7
The NM_006218.4(PIK3CA):c.1143C>A(p.Pro381=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P381P) has been classified as Likely benign.
Frequency
Consequence
NM_006218.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3CA | NM_006218.4 | c.1143C>A | p.Pro381= | splice_region_variant, synonymous_variant | 6/21 | ENST00000263967.4 | |
PIK3CA | XM_006713658.5 | c.1143C>A | p.Pro381= | splice_region_variant, synonymous_variant | 6/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3CA | ENST00000263967.4 | c.1143C>A | p.Pro381= | splice_region_variant, synonymous_variant | 6/21 | 2 | NM_006218.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 152062Hom.: 0 Cov.: 32 FAILED QC
GnomAD4 exome AF: 7.70e-7 AC: 1AN: 1298096Hom.: 0 Cov.: 19 AF XY: 0.00000153 AC XY: 1AN XY: 654772
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74248
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at