16-81910645-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002661.5(PLCG2):c.1859C>T(p.Thr620Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00141 in 1,613,962 control chromosomes in the GnomAD database, including 4 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 (★★).
Frequency
Consequence
NM_002661.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLCG2 | NM_002661.5 | c.1859C>T | p.Thr620Met | missense_variant | Exon 18 of 33 | ENST00000564138.6 | NP_002652.2 | |
PLCG2 | NM_001425749.1 | c.1859C>T | p.Thr620Met | missense_variant | Exon 19 of 34 | NP_001412678.1 | ||
PLCG2 | NM_001425750.1 | c.1859C>T | p.Thr620Met | missense_variant | Exon 18 of 33 | NP_001412679.1 | ||
PLCG2 | NM_001425751.1 | c.1859C>T | p.Thr620Met | missense_variant | Exon 19 of 34 | NP_001412680.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000821 AC: 125AN: 152258Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00118 AC: 293AN: 249294Hom.: 2 AF XY: 0.00112 AC XY: 152AN XY: 135296
GnomAD4 exome AF: 0.00147 AC: 2155AN: 1461586Hom.: 4 Cov.: 32 AF XY: 0.00142 AC XY: 1035AN XY: 727124
GnomAD4 genome AF: 0.000820 AC: 125AN: 152376Hom.: 0 Cov.: 32 AF XY: 0.000752 AC XY: 56AN XY: 74514
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2024 | PLCG2: BP4, BS1 - |
PLCG2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 26, 2021 | 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). - |
Familial cold autoinflammatory syndrome 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2025 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at