chr16-81870866-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002661.5(PLCG2):āc.579C>Gā(p.His193Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000319 in 1,594,418 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H193D) 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLCG2 | NM_002661.5 | c.579C>G | p.His193Gln | missense_variant | 7/33 | ENST00000564138.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCG2 | ENST00000564138.6 | c.579C>G | p.His193Gln | missense_variant | 7/33 | 1 | NM_002661.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000473 AC: 72AN: 152172Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00105 AC: 241AN: 229796Hom.: 2 AF XY: 0.000919 AC XY: 115AN XY: 125120
GnomAD4 exome AF: 0.000302 AC: 436AN: 1442128Hom.: 3 Cov.: 27 AF XY: 0.000288 AC XY: 207AN XY: 717616
GnomAD4 genome AF: 0.000473 AC: 72AN: 152290Hom.: 1 Cov.: 33 AF XY: 0.000537 AC XY: 40AN XY: 74458
ClinVar
Submissions by phenotype
Familial cold autoinflammatory syndrome 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at