16-81785881-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.-47-62C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 1,010,280 control chromosomes in the GnomAD database, including 101,463 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002661.5 intron
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.-47-62C>G | intron_variant | Intron 1 of 32 | ENST00000564138.6 | NP_002652.2 | ||
PLCG2 | NM_001425749.1 | c.-47-62C>G | intron_variant | Intron 2 of 33 | NP_001412678.1 | |||
PLCG2 | NM_001425750.1 | c.-47-62C>G | intron_variant | Intron 1 of 32 | NP_001412679.1 | |||
PLCG2 | NM_001425751.1 | c.-47-62C>G | intron_variant | Intron 2 of 33 | NP_001412680.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.450 AC: 68360AN: 151906Hom.: 15676 Cov.: 32
GnomAD4 exome AF: 0.441 AC: 378352AN: 858256Hom.: 85775 Cov.: 11 AF XY: 0.447 AC XY: 195811AN XY: 437872
GnomAD4 genome AF: 0.450 AC: 68411AN: 152024Hom.: 15688 Cov.: 32 AF XY: 0.455 AC XY: 33820AN XY: 74314
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 68% of patients studied by a panel of primary immunodeficiencies. Number of patients: 60. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at