rs374875207
Positions:
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The ENST00000369519.4(RBM20):c.3655G>A(p.Val1219Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000139 in 1,364,656 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
RBM20
ENST00000369519.4 missense
ENST00000369519.4 missense
Scores
10
6
Clinical Significance
Conservation
PhyloP100: 4.12
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.07776004).
BP6
Variant 10-110835949-G-A is Benign according to our data. Variant chr10-110835949-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 538022.We mark this variant Likely_benign, oryginal submissions are: {Benign=1, Uncertain_significance=1}. Variant chr10-110835949-G-A is described in Lovd as [Likely_benign].
BS2
High AC in GnomAdExome4 at 16 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RBM20 | NM_001134363.3 | c.3655G>A | p.Val1219Met | missense_variant | 14/14 | ENST00000369519.4 | NP_001127835.2 | |
RBM20 | XM_017016103.3 | c.3490G>A | p.Val1164Met | missense_variant | 14/14 | XP_016871592.1 | ||
RBM20 | XM_017016104.3 | c.3271G>A | p.Val1091Met | missense_variant | 14/14 | XP_016871593.1 | ||
RBM20 | XM_047425116.1 | c.3271G>A | p.Val1091Met | missense_variant | 14/14 | XP_047281072.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBM20 | ENST00000369519.4 | c.3655G>A | p.Val1219Met | missense_variant | 14/14 | 1 | NM_001134363.3 | ENSP00000358532 | P1 | |
RBM20 | ENST00000465774.2 | n.596G>A | non_coding_transcript_exon_variant | 2/2 | 4 | |||||
RBM20 | ENST00000480343.2 | n.288G>A | non_coding_transcript_exon_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152222Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000426 AC: 6AN: 140688Hom.: 0 AF XY: 0.0000666 AC XY: 5AN XY: 75020
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GnomAD4 exome AF: 0.0000132 AC: 16AN: 1212316Hom.: 0 Cov.: 16 AF XY: 0.0000132 AC XY: 8AN XY: 605900
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74506
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Cardiomyopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Nov 17, 2022 | - - |
Dilated cardiomyopathy 1DD Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 20, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Uncertain
D
MutationTaster
Benign
N
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Vest4
MVP
ClinPred
T
GERP RS
gMVP
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