16-81786163-T-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_002661.5(PLCG2):c.174T>C(p.Ala58Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 1,613,708 control chromosomes in the GnomAD database, including 394,472 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002661.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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PLCG2 | NM_002661.5 | c.174T>C | p.Ala58Ala | synonymous_variant | Exon 2 of 33 | ENST00000564138.6 | NP_002652.2 | |
PLCG2 | NM_001425749.1 | c.174T>C | p.Ala58Ala | synonymous_variant | Exon 3 of 34 | NP_001412678.1 | ||
PLCG2 | NM_001425750.1 | c.174T>C | p.Ala58Ala | synonymous_variant | Exon 2 of 33 | NP_001412679.1 | ||
PLCG2 | NM_001425751.1 | c.174T>C | p.Ala58Ala | synonymous_variant | Exon 3 of 34 | NP_001412680.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.689 AC: 104674AN: 152006Hom.: 36262 Cov.: 33
GnomAD3 exomes AF: 0.727 AC: 180856AN: 248772Hom.: 66279 AF XY: 0.727 AC XY: 98143AN XY: 135038
GnomAD4 exome AF: 0.699 AC: 1020982AN: 1461586Hom.: 358189 Cov.: 51 AF XY: 0.700 AC XY: 509115AN XY: 727082
GnomAD4 genome AF: 0.689 AC: 104736AN: 152122Hom.: 36283 Cov.: 33 AF XY: 0.696 AC XY: 51787AN XY: 74356
ClinVar
Submissions by phenotype
not provided Benign:2Other:1
Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -
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not specified Benign:2
This variant is classified as Benign based on local population frequency. This variant was detected in 95% of patients studied by a panel of primary immunodeficiencies. Number of patients: 91. Only high quality variants are reported. -
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 -
Familial cold autoinflammatory syndrome 3 Benign:2
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Autoinflammation-PLCG2-associated antibody deficiency-immune dysregulation Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at