rs997329188
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001134363.3(RBM20):c.3636G>A(p.Arg1212=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000054 in 1,480,858 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
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000053 ( 0 hom. )
Consequence
RBM20
NM_001134363.3 synonymous
NM_001134363.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.298
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 10-110835930-G-A is Benign according to our data. Variant chr10-110835930-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 416817.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.298 with no splicing effect.
BS2
?
High AC in GnomAdExome4 at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBM20 | NM_001134363.3 | c.3636G>A | p.Arg1212= | synonymous_variant | 14/14 | ENST00000369519.4 | |
RBM20 | XM_017016103.3 | c.3471G>A | p.Arg1157= | synonymous_variant | 14/14 | ||
RBM20 | XM_017016104.3 | c.3252G>A | p.Arg1084= | synonymous_variant | 14/14 | ||
RBM20 | XM_047425116.1 | c.3252G>A | p.Arg1084= | synonymous_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBM20 | ENST00000369519.4 | c.3636G>A | p.Arg1212= | synonymous_variant | 14/14 | 1 | NM_001134363.3 | P1 | |
RBM20 | ENST00000465774.2 | n.577G>A | non_coding_transcript_exon_variant | 2/2 | 4 | ||||
RBM20 | ENST00000480343.2 | n.269G>A | non_coding_transcript_exon_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152260Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000527 AC: 7AN: 1328598Hom.: 0 Cov.: 22 AF XY: 0.00000455 AC XY: 3AN XY: 659176
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GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74388
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Dilated cardiomyopathy 1DD Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 07, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at