10-110781050-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001134363.3(RBM20):c.441C>T(p.His147His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000374 in 1,551,942 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 (★★).
Frequency
Consequence
NM_001134363.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RBM20 | NM_001134363.3 | c.441C>T | p.His147His | synonymous_variant | Exon 2 of 14 | ENST00000369519.4 | NP_001127835.2 | |
RBM20 | XM_017016103.3 | c.276C>T | p.His92His | synonymous_variant | Exon 2 of 14 | XP_016871592.1 | ||
RBM20 | XM_017016104.3 | c.57C>T | p.His19His | synonymous_variant | Exon 2 of 14 | XP_016871593.1 | ||
RBM20 | XM_047425116.1 | c.57C>T | p.His19His | synonymous_variant | Exon 2 of 14 | XP_047281072.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000146 AC: 23AN: 157184Hom.: 0 AF XY: 0.000108 AC XY: 9AN XY: 83162
GnomAD4 exome AF: 0.0000357 AC: 50AN: 1399590Hom.: 0 Cov.: 32 AF XY: 0.0000261 AC XY: 18AN XY: 690282
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152352Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74492
ClinVar
Submissions by phenotype
not specified Benign:1
p.His147His in exon 2 of RBM20: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue and is not located wi thin the splice consensus sequence. It has been identified in 1/622 of East Asia n chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstit ute.org). -
RBM20-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Dilated cardiomyopathy 1DD Benign:1
- -
Cardiovascular phenotype Benign:1
This alteration is classified as 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