chr16-81900760-C-T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_002661.5(PLCG2):c.1342C>T(p.Arg448Trp) variant causes a missense change. The variant allele was found at a frequency of 0.000139 in 1,602,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R448Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_002661.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLCG2 | NM_002661.5 | c.1342C>T | p.Arg448Trp | missense_variant | 14/33 | ENST00000564138.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCG2 | ENST00000564138.6 | c.1342C>T | p.Arg448Trp | missense_variant | 14/33 | 1 | NM_002661.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000650 AC: 99AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000185 AC: 46AN: 248496Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 134898
GnomAD4 exome AF: 0.0000848 AC: 123AN: 1449838Hom.: 0 Cov.: 31 AF XY: 0.0000613 AC XY: 44AN XY: 718330
GnomAD4 genome AF: 0.000650 AC: 99AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.000646 AC XY: 48AN XY: 74356
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | PLCG2: BS1 - |
Familial cold autoinflammatory syndrome 3 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at