rs879254356
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_006218.4(PIK3CA):c.705C>A(p.Ser235=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,628 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S235S) has been classified as Likely benign.
Frequency
Consequence
NM_006218.4 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.705C>A | p.Ser235= | synonymous_variant | 4/21 | ENST00000263967.4 | |
PIK3CA | XM_006713658.5 | c.705C>A | p.Ser235= | synonymous_variant | 4/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3CA | ENST00000263967.4 | c.705C>A | p.Ser235= | synonymous_variant | 4/21 | 2 | NM_006218.4 | P1 | |
PIK3CA | ENST00000643187.1 | c.705C>A | p.Ser235= | synonymous_variant | 4/22 | ||||
PIK3CA | ENST00000675467.1 | n.3512C>A | non_coding_transcript_exon_variant | 3/20 | |||||
PIK3CA | ENST00000675786.1 | c.705C>A | p.Ser235= | synonymous_variant, NMD_transcript_variant | 4/21 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461628Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727124
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Cowden syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 23, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at