12-10702003-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003651.5(YBX3):c.1010G>A(p.Arg337His) variant causes a missense change. The variant allele was found at a frequency of 0.0000539 in 1,613,854 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. R337C) has been classified as Uncertain significance.
Frequency
Consequence
NM_003651.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
YBX3 | NM_003651.5 | c.1010G>A | p.Arg337His | missense_variant | Exon 8 of 10 | ENST00000228251.9 | NP_003642.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152158Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000104 AC: 26AN: 251156Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135738
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461696Hom.: 0 Cov.: 31 AF XY: 0.0000316 AC XY: 23AN XY: 727148
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152158Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1010G>A (p.R337H) 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 1010, causing the arginine (R) at amino acid position 337 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