chrX-47169430-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005676.5(RBM10):c.133C>A(p.Pro45Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000182 in 1,097,876 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_005676.5 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 |
---|---|---|---|---|---|---|---|---|
RBM10 | NM_005676.5 | c.133C>A | p.Pro45Thr | missense_variant | Exon 3 of 24 | ENST00000377604.8 | NP_005667.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBM10 | ENST00000377604.8 | c.133C>A | p.Pro45Thr | missense_variant | Exon 3 of 24 | 1 | NM_005676.5 | ENSP00000366829.3 | ||
RBM10 | ENST00000329236.8 | c.328C>A | p.Pro110Thr | missense_variant | Exon 3 of 24 | 1 | ENSP00000328848.8 | |||
RBM10 | ENST00000628161.2 | c.133C>A | p.Pro45Thr | missense_variant | Exon 3 of 23 | 1 | ENSP00000486115.1 | |||
RBM10 | ENST00000345781.10 | c.133C>A | p.Pro45Thr | missense_variant | Exon 3 of 23 | 2 | ENSP00000329659.6 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 182281Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66827
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1097876Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 363238
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
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not provided Uncertain:1
This variant has not been reported in the literature in individuals affected with RBM10-related conditions. 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant is present in population databases (rs782797549, gnomAD 0.005%). This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 45 of the RBM10 protein (p.Pro45Thr). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at