20-41162528-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_002660.3(PLCG1):c.589C>T(p.Arg197Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000483 in 1,613,636 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.589C>T | p.Arg197Trp | missense_variant | Exon 5 of 32 | NM_002660.3 | ENSP00000508698.1 | |||
PLCG1 | ENST00000373271.5 | c.589C>T | p.Arg197Trp | missense_variant | Exon 5 of 32 | 1 | ENSP00000362368.1 | |||
PLCG1 | ENST00000244007.7 | c.589C>T | p.Arg197Trp | missense_variant | Exon 6 of 33 | 5 | ENSP00000244007.3 | |||
PLCG1 | ENST00000483646.2 | n.577C>T | non_coding_transcript_exon_variant | Exon 5 of 6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152054Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251392Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135860
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1461582Hom.: 0 Cov.: 31 AF XY: 0.0000413 AC XY: 30AN XY: 727126
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152054Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74274
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.589C>T (p.R197W) alteration is located in exon 5 (coding exon 5) of the PLCG1 gene. This alteration results from a C to T substitution at nucleotide position 589, causing the arginine (R) at amino acid position 197 to be replaced by a tryptophan (W). 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