chr12-113844787-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016196.4(RBM19):c.2666G>A(p.Arg889Lys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,611,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016196.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBM19 | ENST00000261741.10 | c.2666G>A | p.Arg889Lys | missense_variant, splice_region_variant | Exon 23 of 24 | 1 | NM_016196.4 | ENSP00000261741.5 | ||
RBM19 | ENST00000392561.7 | c.2666G>A | p.Arg889Lys | missense_variant, splice_region_variant | Exon 23 of 25 | 1 | ENSP00000376344.3 | |||
RBM19 | ENST00000545145.6 | c.2666G>A | p.Arg889Lys | missense_variant, splice_region_variant | Exon 23 of 25 | 2 | ENSP00000442053.2 | |||
RBM19 | ENST00000552384.1 | n.116G>A | splice_region_variant, non_coding_transcript_exon_variant | Exon 2 of 4 | 3 | ENSP00000449604.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 247602Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134112
GnomAD4 exome AF: 0.00000754 AC: 11AN: 1459180Hom.: 0 Cov.: 33 AF XY: 0.00000827 AC XY: 6AN XY: 725658
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2666G>A (p.R889K) alteration is located in exon 23 (coding exon 23) of the RBM19 gene. This alteration results from a G to A substitution at nucleotide position 2666, causing the arginine (R) at amino acid position 889 to be replaced by a lysine (K). 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