20-41162529-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_002660.3(PLCG1):c.590G>A(p.Arg197Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000093 in 1,613,720 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002660.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLCG1 | ENST00000685551.1 | c.590G>A | p.Arg197Gln | missense_variant | Exon 5 of 32 | NM_002660.3 | ENSP00000508698.1 | |||
PLCG1 | ENST00000373271.5 | c.590G>A | p.Arg197Gln | missense_variant | Exon 5 of 32 | 1 | ENSP00000362368.1 | |||
PLCG1 | ENST00000244007.7 | c.590G>A | p.Arg197Gln | missense_variant | Exon 6 of 33 | 5 | ENSP00000244007.3 | |||
PLCG1 | ENST00000483646.2 | n.578G>A | non_coding_transcript_exon_variant | Exon 5 of 6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152006Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251406Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135868
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461714Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727170
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152006Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74234
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.590G>A (p.R197Q) alteration is located in exon 5 (coding exon 5) of the PLCG1 gene. This alteration results from a G to A substitution at nucleotide position 590, causing the arginine (R) at amino acid position 197 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at