rs1799904
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000439.5(PCSK1):c.239G>T(p.Arg80Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000249 in 1,604,506 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R80Q) has been classified as Likely benign.
Frequency
Consequence
NM_000439.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCSK1 | NM_000439.5 | c.239G>T | p.Arg80Leu | missense_variant | 2/14 | ENST00000311106.8 | NP_000430.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCSK1 | ENST00000311106.8 | c.239G>T | p.Arg80Leu | missense_variant | 2/14 | 1 | NM_000439.5 | ENSP00000308024.2 | ||
PCSK1 | ENST00000508626.5 | c.98G>T | p.Arg33Leu | missense_variant | 2/14 | 2 | ENSP00000421600.1 | |||
PCSK1 | ENST00000509190.1 | c.239G>T | p.Arg80Leu | missense_variant | 3/5 | 4 | ENSP00000427294.1 | |||
ENSG00000251314 | ENST00000502645.2 | n.354+49607C>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251106Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135700
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1452426Hom.: 0 Cov.: 26 AF XY: 0.00000138 AC XY: 1AN XY: 723328
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74278
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at