rs760605118
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6BP7
The NM_001134363.3(RBM20):āc.153G>Cā(p.Pro51=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars). Synonymous variant affecting the same amino acid position (i.e. P51P) has been classified as Likely benign.
Frequency
Genomes: š 0.000048 ( 0 hom., cov: 32)
Exomes š: 0.0015 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
RBM20
NM_001134363.3 synonymous
NM_001134363.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.57
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
?
Variant 10-110644607-G-C is Benign according to our data. Variant chr10-110644607-G-C is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=1.57 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBM20 | NM_001134363.3 | c.153G>C | p.Pro51= | synonymous_variant | 1/14 | ENST00000369519.4 | |
RBM20 | XM_017016103.3 | c.26+1167G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBM20 | ENST00000369519.4 | c.153G>C | p.Pro51= | synonymous_variant | 1/14 | 1 | NM_001134363.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 7AN: 145508Hom.: 0 Cov.: 32 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00150 AC: 1411AN: 939818Hom.: 0 Cov.: 33 AF XY: 0.00140 AC XY: 660AN XY: 472454
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000481 AC: 7AN: 145652Hom.: 0 Cov.: 32 AF XY: 0.0000282 AC XY: 2AN XY: 71046
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at