3-138684790-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_006219.3(PIK3CB):c.2150A>G(p.Asn717Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0011 in 1,612,038 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006219.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3CB | NM_006219.3 | c.2150A>G | p.Asn717Ser | missense_variant | 17/24 | ENST00000674063.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3CB | ENST00000674063.1 | c.2150A>G | p.Asn717Ser | missense_variant | 17/24 | NM_006219.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00101 AC: 153AN: 152194Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00166 AC: 412AN: 248852Hom.: 5 AF XY: 0.00203 AC XY: 273AN XY: 134502
GnomAD4 exome AF: 0.00111 AC: 1624AN: 1459726Hom.: 11 Cov.: 30 AF XY: 0.00131 AC XY: 953AN XY: 726192
GnomAD4 genome ? AF: 0.00100 AC: 153AN: 152312Hom.: 0 Cov.: 31 AF XY: 0.00107 AC XY: 80AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at