rs12784975
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_152309.3(PIK3AP1):āc.1913A>Gā(p.Lys638Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 1,613,944 control chromosomes in the GnomAD database, including 29,672 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_152309.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIK3AP1 | NM_152309.3 | c.1913A>G | p.Lys638Arg | missense_variant | 12/17 | ENST00000339364.10 | NP_689522.2 | |
PIK3AP1 | XM_011539248.2 | c.1913A>G | p.Lys638Arg | missense_variant | 12/16 | XP_011537550.1 | ||
PIK3AP1 | XM_005269499.2 | c.1379A>G | p.Lys460Arg | missense_variant | 11/16 | XP_005269556.1 | ||
PIK3AP1 | XM_047424566.1 | c.1379A>G | p.Lys460Arg | missense_variant | 13/18 | XP_047280522.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIK3AP1 | ENST00000339364.10 | c.1913A>G | p.Lys638Arg | missense_variant | 12/17 | 1 | NM_152309.3 | ENSP00000339826.5 | ||
PIK3AP1 | ENST00000371109.3 | c.710A>G | p.Lys237Arg | missense_variant | 5/10 | 1 | ENSP00000360150.3 | |||
PIK3AP1 | ENST00000371110.6 | c.1379A>G | p.Lys460Arg | missense_variant | 11/16 | 2 | ENSP00000360151.2 | |||
PIK3AP1 | ENST00000489982.1 | n.32A>G | non_coding_transcript_exon_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.174 AC: 26461AN: 152078Hom.: 2611 Cov.: 32
GnomAD3 exomes AF: 0.188 AC: 47224AN: 251030Hom.: 5355 AF XY: 0.181 AC XY: 24594AN XY: 135724
GnomAD4 exome AF: 0.186 AC: 272161AN: 1461748Hom.: 27060 Cov.: 34 AF XY: 0.184 AC XY: 133448AN XY: 727174
GnomAD4 genome AF: 0.174 AC: 26469AN: 152196Hom.: 2612 Cov.: 32 AF XY: 0.168 AC XY: 12533AN XY: 74402
ClinVar
Submissions by phenotype
Infantile spasms Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at