rs854560
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PM2_SupportingBP4_Moderate
The NM_000446(PON1):c.163T>G(p.Leu55Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L55M) has been classified as Benign.
Frequency
Consequence
NM_000446 missense
Scores
Clinical Significance
Conservation
Links
ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PON1 | NM_000446.7 | c.163T>G | p.Leu55Val | missense_variant | 3/9 | ENST00000222381.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PON1 | ENST00000222381.8 | c.163T>G | p.Leu55Val | missense_variant | 3/9 | 1 | NM_000446.7 | P1 | |
PON1 | ENST00000470502.1 | n.283T>G | non_coding_transcript_exon_variant | 2/4 | 4 | ||||
PON1 | ENST00000433729.1 | c.163T>G | p.Leu55Val | missense_variant, NMD_transcript_variant | 3/9 | 3 |
Frequencies
GnomAD3 genomesCov.: 32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460752Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 726782
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out SpliceAI and Pangolin per-transcript scores at