17-39201268-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_000981.4(RPL19):c.61A>G(p.Lys21Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000659 in 151,740 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000981.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPL19 | NM_000981.4 | c.61A>G | p.Lys21Glu | missense_variant | Exon 2 of 6 | ENST00000225430.9 | NP_000972.1 | |
RPL19 | NM_001330200.1 | c.55A>G | p.Lys19Glu | missense_variant | Exon 2 of 6 | NP_001317129.1 | ||
LOC124903996 | XR_007065745.1 | n.-54T>C | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151740Hom.: 0 Cov.: 31
GnomAD4 exome Cov.: 30
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151740Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74062
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant has not been reported in the literature in individuals affected with RPL19-related conditions. This sequence change replaces lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 21 of the RPL19 protein (p.Lys21Glu). This variant is not present in population databases (gnomAD no frequency). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at