chr10-96602305-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_152309.3(PIK3AP1):c.2335G>A(p.Val779Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00035 in 1,607,246 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V779L) has been classified as Uncertain significance.
Frequency
Consequence
NM_152309.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3AP1 | NM_152309.3 | c.2335G>A | p.Val779Met | missense_variant | 16/17 | ENST00000339364.10 | |
LOC105378443 | XR_946220.4 | n.1447-5371C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3AP1 | ENST00000339364.10 | c.2335G>A | p.Val779Met | missense_variant | 16/17 | 1 | NM_152309.3 | P1 | |
PIK3AP1 | ENST00000371109.3 | c.1132G>A | p.Val378Met | missense_variant | 9/10 | 1 | |||
PIK3AP1 | ENST00000371110.6 | c.1801G>A | p.Val601Met | missense_variant | 15/16 | 2 | |||
PIK3AP1 | ENST00000467625.5 | n.532G>A | non_coding_transcript_exon_variant | 5/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000302 AC: 46AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000393 AC: 96AN: 244474Hom.: 1 AF XY: 0.000408 AC XY: 54AN XY: 132394
GnomAD4 exome AF: 0.000355 AC: 516AN: 1455002Hom.: 1 Cov.: 30 AF XY: 0.000344 AC XY: 249AN XY: 723952
GnomAD4 genome ? AF: 0.000309 AC: 47AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2022 | The c.2335G>A (p.V779M) alteration is located in exon 16 (coding exon 16) of the PIK3AP1 gene. This alteration results from a G to A substitution at nucleotide position 2335, causing the valine (V) at amino acid position 779 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Infantile spasms Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 16, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at