rs1071644
Variant summary
Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_002661.5(PLCG2):c.3093T>C(p.Asn1031Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 1,613,270 control chromosomes in the GnomAD database, including 200,986 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
Publications
- autoinflammation-PLCG2-associated antibody deficiency-immune dysregulationInheritance: AD Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet, G2P
- familial cold autoinflammatory syndrome 3Inheritance: AD Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P
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ACMG classification
Our verdict: Benign. The variant received -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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PLCG2 | NM_002661.5 | c.3093T>C | p.Asn1031Asn | synonymous_variant | Exon 28 of 33 | ENST00000564138.6 | NP_002652.2 | |
PLCG2 | NM_001425749.1 | c.3093T>C | p.Asn1031Asn | synonymous_variant | Exon 29 of 34 | NP_001412678.1 | ||
PLCG2 | NM_001425750.1 | c.3093T>C | p.Asn1031Asn | synonymous_variant | Exon 28 of 33 | NP_001412679.1 | ||
PLCG2 | NM_001425751.1 | c.3093T>C | p.Asn1031Asn | synonymous_variant | Exon 29 of 34 | NP_001412680.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.394 AC: 59920AN: 151988Hom.: 14054 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.445 AC: 110907AN: 249252 AF XY: 0.458 show subpopulations
GnomAD4 exome AF: 0.499 AC: 728819AN: 1461164Hom.: 186935 Cov.: 36 AF XY: 0.499 AC XY: 363069AN XY: 726914 show subpopulations
GnomAD4 genome AF: 0.394 AC: 59912AN: 152106Hom.: 14051 Cov.: 32 AF XY: 0.392 AC XY: 29119AN XY: 74346 show subpopulations
ClinVar
Submissions by phenotype
not specified Benign:5
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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 58% of patients studied by a panel of primary immunodeficiencies. Number of patients: 56. Only high quality variants are reported. -
not provided Benign:2Other:1
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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. -
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