16-81921184-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002661.5(PLCG2):c.2236-14C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 1,490,582 control chromosomes in the GnomAD database, including 242,159 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002661.5 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.2236-14C>G | intron_variant | Intron 20 of 32 | ENST00000564138.6 | NP_002652.2 | ||
PLCG2 | NM_001425749.1 | c.2236-14C>G | intron_variant | Intron 21 of 33 | NP_001412678.1 | |||
PLCG2 | NM_001425750.1 | c.2236-14C>G | intron_variant | Intron 20 of 32 | NP_001412679.1 | |||
PLCG2 | NM_001425751.1 | c.2236-14C>G | intron_variant | Intron 21 of 33 | NP_001412680.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.496 AC: 75191AN: 151620Hom.: 20800 Cov.: 31
GnomAD3 exomes AF: 0.595 AC: 141304AN: 237632Hom.: 42541 AF XY: 0.594 AC XY: 76689AN XY: 129028
GnomAD4 exome AF: 0.573 AC: 766775AN: 1338850Hom.: 221362 Cov.: 21 AF XY: 0.572 AC XY: 384704AN XY: 672210
GnomAD4 genome AF: 0.496 AC: 75217AN: 151732Hom.: 20797 Cov.: 31 AF XY: 0.501 AC XY: 37186AN XY: 74176
ClinVar
Submissions by phenotype
not specified Benign:5
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
- -
- -
- -
This variant is classified as Benign based on local population frequency. This variant was detected in 90% of patients studied by a panel of primary immunodeficiencies. Number of patients: 86. Only high quality variants are reported. -
not provided Benign:2
- -
- -
Familial cold autoinflammatory syndrome 3 Benign:2
- -
- -
Familial cold autoinflammatory syndrome 3;C3553961:Autoinflammation-PLCG2-associated antibody deficiency-immune dysregulation Benign:1
- -
Autoinflammation-PLCG2-associated antibody deficiency-immune dysregulation Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at