10-110812598-G-A
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_001134363.3(RBM20):c.2201G>A(p.Arg734Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000619 in 1,551,572 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 Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R734W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001134363.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBM20 | NM_001134363.3 | c.2201G>A | p.Arg734Gln | missense_variant | 9/14 | ENST00000369519.4 | |
RBM20 | XM_017016103.3 | c.2036G>A | p.Arg679Gln | missense_variant | 9/14 | ||
RBM20 | XM_017016104.3 | c.1817G>A | p.Arg606Gln | missense_variant | 9/14 | ||
RBM20 | XM_047425116.1 | c.1817G>A | p.Arg606Gln | missense_variant | 9/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBM20 | ENST00000369519.4 | c.2201G>A | p.Arg734Gln | missense_variant | 9/14 | 1 | NM_001134363.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000769 AC: 12AN: 156036Hom.: 0 AF XY: 0.0000846 AC XY: 7AN XY: 82734
GnomAD4 exome AF: 0.0000436 AC: 61AN: 1399384Hom.: 0 Cov.: 32 AF XY: 0.0000507 AC XY: 35AN XY: 690202
GnomAD4 genome AF: 0.000230 AC: 35AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74362
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 17, 2019 | The p.Arg734Gln variant in RBM20 is classified as likely benign because it has been identified in 0.1% (19/16596) of African chromosomes by gnomAD (http://gnomad.broadinstitute.org). ACMG/AMP Criteria applied: BS1. - |
Dilated cardiomyopathy 1DD Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2020 | This variant is associated with the following publications: (PMID: 32880476) - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at