20-41160144-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002660.3(PLCG1):c.503G>A(p.Arg168His) variant causes a missense change. The variant allele was found at a frequency of 0.0000366 in 1,613,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict 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 -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLCG1 | ENST00000685551.1 | c.503G>A | p.Arg168His | missense_variant | Exon 4 of 32 | NM_002660.3 | ENSP00000508698.1 | |||
PLCG1 | ENST00000373271.5 | c.503G>A | p.Arg168His | missense_variant | Exon 4 of 32 | 1 | ENSP00000362368.1 | |||
PLCG1 | ENST00000244007.7 | c.503G>A | p.Arg168His | missense_variant | Exon 5 of 33 | 5 | ENSP00000244007.3 | |||
PLCG1 | ENST00000483646.2 | n.413G>A | non_coding_transcript_exon_variant | Exon 4 of 6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251404Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135884
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461780Hom.: 0 Cov.: 31 AF XY: 0.0000316 AC XY: 23AN XY: 727204
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.503G>A (p.R168H) alteration is located in exon 4 (coding exon 4) of the PLCG1 gene. This alteration results from a G to A substitution at nucleotide position 503, causing the arginine (R) at amino acid position 168 to be replaced by a histidine (H). 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