2-198084019-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006226.4(PLCL1):c.502C>G(p.Leu168Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,461,854 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006226.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLCL1 | NM_006226.4 | c.502C>G | p.Leu168Val | missense_variant | 2/6 | ENST00000428675.6 | |
PLCL1 | XM_005246643.5 | c.280C>G | p.Leu94Val | missense_variant | 2/6 | ||
PLCL1 | XM_005246644.5 | c.265C>G | p.Leu89Val | missense_variant | 2/6 | ||
PLCL1 | XM_017004339.3 | c.265C>G | p.Leu89Val | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCL1 | ENST00000428675.6 | c.502C>G | p.Leu168Val | missense_variant | 2/6 | 1 | NM_006226.4 | P1 | |
PLCL1 | ENST00000487695.6 | c.280C>G | p.Leu94Val | missense_variant | 2/6 | 5 | |||
PLCL1 | ENST00000435320.1 | c.*274C>G | 3_prime_UTR_variant, NMD_transcript_variant | 3/7 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461854Hom.: 0 Cov.: 34 AF XY: 0.0000138 AC XY: 10AN XY: 727236
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2022 | The c.502C>G (p.L168V) alteration is located in exon 2 (coding exon 2) of the PLCL1 gene. This alteration results from a C to G substitution at nucleotide position 502, causing the leucine (L) at amino acid position 168 to be replaced by a valine (V). 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