10-110784442-G-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001134363.3(RBM20):c.1429+10G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000271 in 1,547,232 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: 33)
Exomes 𝑓: 0.000028 ( 0 hom. )
Consequence
RBM20
NM_001134363.3 intron
NM_001134363.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.212
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 10-110784442-G-T is Benign according to our data. Variant chr10-110784442-G-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 298796.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1}.
BS1
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.000028 (39/1394930) while in subpopulation EAS AF= 0.00106 (38/35716). AF 95% confidence interval is 0.000796. There are 0 homozygotes in gnomad4_exome. There are 18 alleles in male gnomad4_exome subpopulation. Median coverage is 29. This position pass quality control queck.
BS2
High AC in GnomAdExome4 at 39 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBM20 | NM_001134363.3 | c.1429+10G>T | intron_variant | ENST00000369519.4 | |||
RBM20 | XM_017016103.3 | c.1264+10G>T | intron_variant | ||||
RBM20 | XM_017016104.3 | c.1045+10G>T | intron_variant | ||||
RBM20 | XM_047425116.1 | c.1045+10G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBM20 | ENST00000369519.4 | c.1429+10G>T | intron_variant | 1 | NM_001134363.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000846 AC: 13AN: 153660Hom.: 0 AF XY: 0.0000613 AC XY: 5AN XY: 81522
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GnomAD4 exome AF: 0.0000280 AC: 39AN: 1394930Hom.: 0 Cov.: 29 AF XY: 0.0000261 AC XY: 18AN XY: 688346
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152302Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74474
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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
Dilated cardiomyopathy 1DD Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 24, 2023 | - - |
Computational scores
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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