chr10-110644449-C-T
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001134363.3(RBM20):c.-6C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000146 in 1,483,238 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00016 ( 1 hom. )
Consequence
RBM20
NM_001134363.3 5_prime_UTR
NM_001134363.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.374
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant 10-110644449-C-T is Benign according to our data. Variant chr10-110644449-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 43962.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomAdExome4 at 214 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBM20 | NM_001134363.3 | c.-6C>T | 5_prime_UTR_variant | 1/14 | ENST00000369519.4 | ||
RBM20 | XM_017016103.3 | c.26+1009C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBM20 | ENST00000369519.4 | c.-6C>T | 5_prime_UTR_variant | 1/14 | 1 | NM_001134363.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152182Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000694 AC: 6AN: 86428Hom.: 0 AF XY: 0.0000818 AC XY: 4AN XY: 48926
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GnomAD4 exome AF: 0.000161 AC: 214AN: 1331056Hom.: 1 Cov.: 31 AF XY: 0.000176 AC XY: 115AN XY: 655006
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74352
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jul 31, 2012 | -6C>T in the 5' UTR of RBM20: This variant is located in the 5' UTR and varian ts in regulatory regions could have an effect on transcriptional or translationa l efficiency. However, no variants in this region of RBM20 have been found to be pathogenic in individuals with cardiomyopathy. Therefore, this variant is not e xpected to have clinical significance. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 27, 2022 | See Variant Classification Assertion Criteria. - |
Computational scores
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BayesDel_noAF
Benign
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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