chr10-96602329-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_152309.3(PIK3AP1):āc.2311A>Gā(p.Met771Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,611,430 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_152309.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIK3AP1 | NM_152309.3 | c.2311A>G | p.Met771Val | missense_variant | 16/17 | ENST00000339364.10 | NP_689522.2 | |
LOC105378443 | XR_946220.4 | n.1447-5347T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIK3AP1 | ENST00000339364.10 | c.2311A>G | p.Met771Val | missense_variant | 16/17 | 1 | NM_152309.3 | ENSP00000339826 | P1 | |
PIK3AP1 | ENST00000371109.3 | c.1108A>G | p.Met370Val | missense_variant | 9/10 | 1 | ENSP00000360150 | |||
PIK3AP1 | ENST00000371110.6 | c.1777A>G | p.Met593Val | missense_variant | 15/16 | 2 | ENSP00000360151 | |||
PIK3AP1 | ENST00000467625.5 | n.508A>G | non_coding_transcript_exon_variant | 5/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249432Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 134940
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1459258Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 725996
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at