chr1-204424895-G-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001377334.1(PIK3C2B):c.4862C>G(p.Thr1621Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000318 in 1,614,208 control chromosomes in the GnomAD database, including 4 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 (★★). Synonymous variant affecting the same amino acid position (i.e. T1621T) has been classified as Likely benign.
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.4862C>G | p.Thr1621Ser | missense_variant | 33/33 | ENST00000684373.1 | |
PIK3C2B | NM_002646.4 | c.4862C>G | p.Thr1621Ser | missense_variant | 35/35 | ||
PIK3C2B | NM_001377335.1 | c.4778C>G | p.Thr1593Ser | missense_variant | 36/36 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3C2B | ENST00000684373.1 | c.4862C>G | p.Thr1621Ser | missense_variant | 33/33 | NM_001377334.1 | P1 | ||
PPP1R15B-AS1 | ENST00000443515.1 | n.147-10442G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00158 AC: 241AN: 152208Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000402 AC: 101AN: 251226Hom.: 1 AF XY: 0.000228 AC XY: 31AN XY: 135812
GnomAD4 exome AF: 0.000185 AC: 270AN: 1461882Hom.: 2 Cov.: 31 AF XY: 0.000151 AC XY: 110AN XY: 727240
GnomAD4 genome ? AF: 0.00160 AC: 243AN: 152326Hom.: 2 Cov.: 32 AF XY: 0.00141 AC XY: 105AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 10, 2018 | - - |
PIK3C2B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 25, 2019 | 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