10-110799884-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R589W) has been classified as Likely benign.
Frequency
Consequence
NM_001134363.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBM20 | NM_001134363.3 | c.1766G>A | p.Arg589Gln | missense_variant | 7/14 | ENST00000369519.4 | |
RBM20 | XM_017016103.3 | c.1601G>A | p.Arg534Gln | missense_variant | 7/14 | ||
RBM20 | XM_017016104.3 | c.1382G>A | p.Arg461Gln | missense_variant | 7/14 | ||
RBM20 | XM_047425116.1 | c.1382G>A | p.Arg461Gln | missense_variant | 7/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBM20 | ENST00000369519.4 | c.1766G>A | p.Arg589Gln | missense_variant | 7/14 | 1 | NM_001134363.3 | P1 |
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
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 17, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 04, 2023 | - - |
Cardiomyopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Jun 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at