19-17863001-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_000980.4(RPL18A):c.412C>T(p.Arg138Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000788 in 1,611,778 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R138H) has been classified as Uncertain significance.
Frequency
Consequence
NM_000980.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL18A | NM_000980.4 | c.412C>T | p.Arg138Cys | missense_variant | 4/5 | ENST00000222247.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL18A | ENST00000222247.10 | c.412C>T | p.Arg138Cys | missense_variant | 4/5 | 1 | NM_000980.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000769 AC: 19AN: 247018Hom.: 0 AF XY: 0.0000894 AC XY: 12AN XY: 134264
GnomAD4 exome AF: 0.0000788 AC: 115AN: 1459638Hom.: 0 Cov.: 30 AF XY: 0.0000744 AC XY: 54AN XY: 726152
GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 08, 2023 | The c.412C>T (p.R138C) alteration is located in exon 4 (coding exon 4) of the RPL18A gene. This alteration results from a C to T substitution at nucleotide position 412, causing the arginine (R) at amino acid position 138 to be replaced by a cysteine (C). 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