10-110799884-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_001134363.3(RBM20):c.1766G>A(p.Arg589Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,551,930 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001134363.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RBM20 | NM_001134363.3 | c.1766G>A | p.Arg589Gln | missense_variant | Exon 7 of 14 | ENST00000369519.4 | NP_001127835.2 | |
RBM20 | XM_017016103.3 | c.1601G>A | p.Arg534Gln | missense_variant | Exon 7 of 14 | XP_016871592.1 | ||
RBM20 | XM_017016104.3 | c.1382G>A | p.Arg461Gln | missense_variant | Exon 7 of 14 | XP_016871593.1 | ||
RBM20 | XM_047425116.1 | c.1382G>A | p.Arg461Gln | missense_variant | Exon 7 of 14 | XP_047281072.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000316 AC: 5AN: 158246Hom.: 0 AF XY: 0.0000240 AC XY: 2AN XY: 83410
GnomAD4 exome AF: 0.000115 AC: 161AN: 1399764Hom.: 0 Cov.: 30 AF XY: 0.0000913 AC XY: 63AN XY: 690350
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74334
ClinVar
Submissions by phenotype
Dilated cardiomyopathy 1DD Uncertain:1Benign:1
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Cardiomyopathy Uncertain:1
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Cardiovascular phenotype Uncertain:1
The p.R589Q variant (also known as c.1766G>A), located in coding exon 7 of the RBM20 gene, results from a G to A substitution at nucleotide position 1766. The arginine at codon 589 is replaced by glutamine, an amino acid with highly similar properties. This alteration has been reported in a hypertrophic cardiomyopathy (HCM) cohort; however, clinical details were limited (Lopes LR et al. Heart, 2015 Feb;101:294-301). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the available evidence, the clinical significance of this variant remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at