12-10702120-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003651.5(YBX3):c.893G>A(p.Arg298His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000688 in 1,613,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R298G) has been classified as Uncertain significance.
Frequency
Consequence
NM_003651.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
YBX3 | NM_003651.5 | c.893G>A | p.Arg298His | missense_variant | Exon 8 of 10 | ENST00000228251.9 | NP_003642.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152120Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000638 AC: 16AN: 250674Hom.: 0 AF XY: 0.0000812 AC XY: 11AN XY: 135444
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461472Hom.: 0 Cov.: 32 AF XY: 0.0000646 AC XY: 47AN XY: 727054
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152120Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.893G>A (p.R298H) alteration is located in exon 8 (coding exon 8) of the YBX3 gene. This alteration results from a G to A substitution at nucleotide position 893, causing the arginine (R) at amino acid position 298 to be replaced by a histidine (H). 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