NM_006218.4:c.705C>A
Variant summary
Our verdict is Benign. The variant received -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_006218.4(PIK3CA):c.705C>A(p.Ser235Ser) 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
Publications
- overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genesInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- megalencephaly-capillary malformation-polymicrogyria syndromeInheritance: AD Classification: STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
- vascular malformationInheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
- Cowden diseaseInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Cowden syndrome 5Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
- familial ovarian cancerInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
- hereditary breast carcinomaInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
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ACMG classification
Our verdict: Benign. The variant received -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIK3CA | ENST00000263967.4 | c.705C>A | p.Ser235Ser | synonymous_variant | Exon 4 of 21 | 2 | NM_006218.4 | ENSP00000263967.3 | ||
PIK3CA | ENST00000643187.1 | c.705C>A | p.Ser235Ser | synonymous_variant | Exon 4 of 22 | ENSP00000493507.1 | ||||
PIK3CA | ENST00000675467.1 | n.3512C>A | non_coding_transcript_exon_variant | Exon 3 of 20 | ||||||
PIK3CA | ENST00000675786.1 | n.705C>A | non_coding_transcript_exon_variant | Exon 4 of 21 | ENSP00000502323.1 |
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 show subpopulations
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Cowden syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at