rs114618894
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002661.5(PLCG2):c.2542C>T(p.Leu848Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000982 in 1,609,336 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L848L) has been classified 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLCG2 | NM_002661.5 | c.2542C>T | p.Leu848Phe | missense_variant | 24/33 | ENST00000564138.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCG2 | ENST00000564138.6 | c.2542C>T | p.Leu848Phe | missense_variant | 24/33 | 1 | NM_002661.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00476 AC: 724AN: 152216Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00123 AC: 306AN: 249564Hom.: 2 AF XY: 0.000872 AC XY: 118AN XY: 135396
GnomAD4 exome AF: 0.000585 AC: 853AN: 1457002Hom.: 5 Cov.: 28 AF XY: 0.000499 AC XY: 362AN XY: 725242
GnomAD4 genome AF: 0.00477 AC: 727AN: 152334Hom.: 8 Cov.: 33 AF XY: 0.00438 AC XY: 326AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 19, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 29, 2023 | - - |
Autoinflammation-PLCG2-associated antibody deficiency-immune dysregulation Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 24, 2020 | - - |
Familial cold autoinflammatory syndrome 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at