6-30619786-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_014046.4(MRPS18B):c.265C>T(p.Arg89Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000235 in 1,614,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. 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. R89Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_014046.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPS18B | ENST00000259873.5 | c.265C>T | p.Arg89Trp | missense_variant | Exon 3 of 7 | 1 | NM_014046.4 | ENSP00000259873.4 | ||
MRPS18B | ENST00000472267.5 | n.386C>T | non_coding_transcript_exon_variant | Exon 2 of 5 | 1 | |||||
MRPS18B | ENST00000472229.1 | n.299C>T | non_coding_transcript_exon_variant | Exon 3 of 7 | 3 | |||||
MRPS18B | ENST00000492316.5 | n.288C>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251260Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135824
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461850Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 727230
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.265C>T (p.R89W) alteration is located in exon 3 (coding exon 3) of the MRPS18B gene. This alteration results from a C to T substitution at nucleotide position 265, causing the arginine (R) at amino acid position 89 to be replaced by a tryptophan (W). 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