chr1-204431758-G-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001377334.1(PIK3C2B):c.4191C>A(p.His1397Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000267 in 1,614,126 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H1397R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001377334.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3C2B | NM_001377334.1 | c.4191C>A | p.His1397Gln | missense_variant | 28/33 | ENST00000684373.1 | |
PIK3C2B | NM_002646.4 | c.4191C>A | p.His1397Gln | missense_variant | 30/35 | ||
PIK3C2B | NM_001377335.1 | c.4107C>A | p.His1369Gln | missense_variant | 31/36 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3C2B | ENST00000684373.1 | c.4191C>A | p.His1397Gln | missense_variant | 28/33 | NM_001377334.1 | P1 | ||
PPP1R15B-AS1 | ENST00000443515.1 | n.147-3579G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00139 AC: 212AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000390 AC: 98AN: 251492Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135920
GnomAD4 exome AF: 0.000149 AC: 218AN: 1461844Hom.: 1 Cov.: 32 AF XY: 0.000133 AC XY: 97AN XY: 727226
GnomAD4 genome AF: 0.00140 AC: 213AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.00117 AC XY: 87AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 07, 2018 | - - |
PIK3C2B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 29, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at