10-96648752-C-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_152309.3(PIK3AP1):c.1092G>C(p.Ala364Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000683 in 1,610,686 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. A364A) has been classified as Benign.
Frequency
Consequence
NM_152309.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIK3AP1 | NM_152309.3 | c.1092G>C | p.Ala364Ala | synonymous_variant | Exon 7 of 17 | ENST00000339364.10 | NP_689522.2 | |
PIK3AP1 | XM_011539248.2 | c.1092G>C | p.Ala364Ala | synonymous_variant | Exon 7 of 16 | XP_011537550.1 | ||
PIK3AP1 | XM_005269499.2 | c.558G>C | p.Ala186Ala | synonymous_variant | Exon 6 of 16 | XP_005269556.1 | ||
PIK3AP1 | XM_047424566.1 | c.558G>C | p.Ala186Ala | synonymous_variant | Exon 8 of 18 | XP_047280522.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIK3AP1 | ENST00000339364.10 | c.1092G>C | p.Ala364Ala | synonymous_variant | Exon 7 of 17 | 1 | NM_152309.3 | ENSP00000339826.5 | ||
PIK3AP1 | ENST00000371110.6 | c.558G>C | p.Ala186Ala | synonymous_variant | Exon 6 of 16 | 2 | ENSP00000360151.2 | |||
PIK3AP1 | ENST00000468783.1 | n.738G>C | non_coding_transcript_exon_variant | Exon 6 of 8 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000364 AC: 9AN: 247390Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133836
GnomAD4 exome AF: 0.00000686 AC: 10AN: 1458494Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 725556
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
Infantile spasms Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at