rs140843691
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_152309.3(PIK3AP1):c.1302G>T(p.Ser434=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,666 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S434S) has been classified as Likely benign.
Frequency
Consequence
NM_152309.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3AP1 | NM_152309.3 | c.1302G>T | p.Ser434= | synonymous_variant | 8/17 | ENST00000339364.10 | |
PIK3AP1 | XM_011539248.2 | c.1302G>T | p.Ser434= | synonymous_variant | 8/16 | ||
PIK3AP1 | XM_005269499.2 | c.768G>T | p.Ser256= | synonymous_variant | 7/16 | ||
PIK3AP1 | XM_047424566.1 | c.768G>T | p.Ser256= | synonymous_variant | 9/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3AP1 | ENST00000339364.10 | c.1302G>T | p.Ser434= | synonymous_variant | 8/17 | 1 | NM_152309.3 | P1 | |
PIK3AP1 | ENST00000371110.6 | c.768G>T | p.Ser256= | synonymous_variant | 7/16 | 2 | |||
PIK3AP1 | ENST00000468783.1 | n.948G>T | non_coding_transcript_exon_variant | 7/8 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461666Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727134
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at