chr1-204431759-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001377334.1(PIK3C2B):c.4190A>G(p.His1397Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,461,880 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H1397Q) has been classified as Likely benign.
Frequency
Consequence
NM_001377334.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3C2B | NM_001377334.1 | c.4190A>G | p.His1397Arg | missense_variant | 28/33 | ENST00000684373.1 | |
PIK3C2B | NM_002646.4 | c.4190A>G | p.His1397Arg | missense_variant | 30/35 | ||
PIK3C2B | NM_001377335.1 | c.4106A>G | p.His1369Arg | missense_variant | 31/36 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3C2B | ENST00000684373.1 | c.4190A>G | p.His1397Arg | missense_variant | 28/33 | NM_001377334.1 | P1 | ||
PPP1R15B-AS1 | ENST00000443515.1 | n.147-3578T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251494Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135922
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461880Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727242
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.4190A>G (p.H1397R) alteration is located in exon 29 (coding exon 27) of the PIK3C2B gene. This alteration results from a A to G substitution at nucleotide position 4190, causing the histidine (H) at amino acid position 1397 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at