rs201779890
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PP5_StrongBP4
The NM_005105.5(RBM8A):c.67+32G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00482 in 1,603,802 control chromosomes in the GnomAD database, including 52 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as other (★★).
Frequency
Genomes: 𝑓 0.0049 ( 5 hom., cov: 31)
Exomes 𝑓: 0.0048 ( 47 hom. )
Consequence
RBM8A
NM_005105.5 intron
NM_005105.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.828
Genes affected
RBM8A (HGNC:9905): (RNA binding motif protein 8A) This gene encodes a protein with a conserved RNA-binding motif. The protein is found predominantly in the nucleus, although it is also present in the cytoplasm. It is preferentially associated with mRNAs produced by splicing, including both nuclear mRNAs and newly exported cytoplasmic mRNAs. It is thought that the protein remains associated with spliced mRNAs as a tag to indicate where introns had been present, thus coupling pre- and post-mRNA splicing events. Previously, it was thought that two genes encode this protein, RBM8A and RBM8B; it is now thought that the RBM8B locus is a pseudogene. There are two alternate translation start codons with this gene, which result in two forms of the protein. An allele mutation and a low-frequency noncoding single-nucleotide polymorphism (SNP) in this gene cause thrombocytopenia-absent radius (TAR) syndrome. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PP5
Variant 1-145927328-C-G is Pathogenic according to our data. Variant chr1-145927328-C-G is described in ClinVar as [other]. Clinvar id is 30465.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic_low_penetrance=1, not_provided=1, Pathogenic=9, Likely_pathogenic=1}.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36). . Strength limited to SUPPORTING due to the PP5.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RBM8A | NM_005105.5 | c.67+32G>C | intron_variant | ENST00000583313.7 | NP_005096.1 | |||
LIX1L-AS1 | NR_147182.1 | n.381C>G | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBM8A | ENST00000583313.7 | c.67+32G>C | intron_variant | 1 | NM_005105.5 | ENSP00000463058.2 | ||||
ENSG00000280778 | ENST00000625258.1 | c.-30+39C>G | intron_variant | 5 | ENSP00000487094.1 |
Frequencies
GnomAD3 genomes AF: 0.00489 AC: 744AN: 152140Hom.: 5 Cov.: 31
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GnomAD3 exomes AF: 0.00547 AC: 1281AN: 234162Hom.: 8 AF XY: 0.00545 AC XY: 688AN XY: 126236
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GnomAD4 exome AF: 0.00482 AC: 6994AN: 1451544Hom.: 47 Cov.: 31 AF XY: 0.00475 AC XY: 3422AN XY: 720966
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GnomAD4 genome AF: 0.00489 AC: 744AN: 152258Hom.: 5 Cov.: 31 AF XY: 0.00533 AC XY: 397AN XY: 74438
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ClinVar
Significance: Pathogenic/Likely pathogenic/Pathogenic, low penetrance
Submissions summary: Pathogenic:17Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Radial aplasia-thrombocytopenia syndrome Pathogenic:8Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Pathogenic, low penetrance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | This sequence change falls in intron 1 of the RBM8A gene. It does not directly change the encoded amino acid sequence of the RBM8A protein. Experimental studies have reported that this variant leads to a partial decrease in RBM8A expression in vitro, possibly by disrupting a transcription factor binding site (PMID: 22366785). This variant is present in population databases (rs201779890, gnomAD 2.3%), including at least one homozygous and/or hemizygous individual. This variant has been observed on the opposite chromosome (in trans) from a whole gene deletion of RBM8A in several individuals affected with TAR syndrome (PMID: 22366785). However, it has been reported as homozygous in an unaffected parent (PMID: 22366785). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 30465). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, this variant is reported to cause disease. However, as this variant is associated with a lower penetrance than other pathogenic alleles in the RBM8A gene, it has been classified as Pathogenic (low penetrance). - |
Pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 14, 2018 | The c.67+32G>C variant in RBM8A has been reported in >25 individuals with thromb ocytopenia with absent radius (TAR) syndrome, all of whom had a submicroscopic d eletion encompassing the RBM8A gene on the second allele (Albers 2012, Manukjan 2017), suggesting that compound heterozygosity for this variant and a loss of fu nction variant in RBM8A is disease causing. In vitro studies demonstrated that t his variant may lead to reduced gene expression (Albers 2012). Although this var iant has also been identified in 2.5% (562/24044) of Finnish and 0.7% (883/11850 8) of other European chromosomes, including 11 homozygotes, by the Genome Aggreg ation Database (gnomAD, http://exac.broadinstitute.org; dbSNP rs201779890), loss of function variants in RBM8A are very rare in large population studies, sugges ting that compound heterozygosity for the c.67+32G>C variant and a loss of funct ion variant in RBM8A is rare. Compound heterozygosity for this variant and a los s-of-function variant in RBM8A is strongly associated with TAR syndrome. Note th at individuals that are homozygous for this variant are not expected to have fea tures of TAR syndrome. In summary, this variant is pathogenic for TAR syndrome i n an autosomal recessive manner. ACMG/AMP Criteria applied: PS3, PM3_VeryStrong. - |
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 13, 2022 | - - |
Pathogenic, no assertion criteria provided | curation | Reproductive Health Research and Development, BGI Genomics | Jan 06, 2020 | NG_032654.2(NM_005105.4):c.67+32G>C in the RBM8A gene has an allele frequency of 0.023 in European(non-Finnish) subpopulation in the gnomAD database. Experimental studies have reported that c.67+32G>C leads to a partial decrease in RBM8A expression in vitro, possibly by disrupting a transcription factor binding site (PMID: 22366785). It was detected in multiple individuals with Radial aplasia-thrombocytopenia syndrome, compound heterozygous with a submicroscopic deletion encompassing the RBM8A gene (PMID: 22366785). Taken together, we interprete this variant as Pathogenic/Likely pathogenic variant. ACMG/AMP criteria applied: PS3; PM3_Strong; PP4. - |
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 25, 2023 | Variant summary: RBM8A c.67+32G>C is located at a position not widely known to affect splicing. 4/4 computational tools predict no significant impact on normal splicing. The variant allele was found at a frequency of 0.0055 in 234162 control chromosomes in the gnomAD database, including 8 homozygotes. Homozygotes in this variant are not expected to have features of TAR due to compound inheritance mechanism of this disease. c.67+32G>C has been reported to segregate with disease in the literature in multiple individuals affected with Radial Aplasia-Thrombocytopenia Syndrome, combined with a 1q21.1 deletion (Albers_2012). These data indicate that the variant is very likely to be associated with disease. Experimental studies suggest a reduced expression of the RBM8A protein and possibly disrupting a transcription factor binding site (Albers_2012). Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic (n=8) and likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Apr 19, 2023 | This variant was identified as hemizygous in trans with a 414kb Deletion causative for the TAR Syndrome._x000D_ Criteria applied: PM3_VSTR, PS3, PP4 - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 26, 2012 | - - |
not provided Pathogenic:7
Pathogenic, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Apr 19, 2024 | BS1, BS2, PM3_very_strong, PS3, PS4_supporting - |
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen | Oct 23, 2020 | - - |
Likely pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Nov 22, 2024 | Observed multiple times with a null pathogenic variant on the opposite allele (in trans) in unrelated patients with TAR syndrome in the published literature (PMID: 22366785, 28857120); Published functional studies suggest a damaging effect due to disruption of a transcription factor binding site and reduced expression of the resulting protein, consistent with a hypomorphic allele (PMID: 22366785); In silico analysis supports that this variant does not alter splicing; This variant is associated with the following publications: (PMID: 30609409, 27320760, 34906519, 22366785, 30385887, 27348543, 32109542, 32227665, 34958143, 36077017, 28857120) - |
Pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 26, 2016 | - - |
Likely pathogenic, no assertion criteria provided | literature only | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Dec 24, 2022 | - - |
Likely pathogenic, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Global developmental delay;C1850049:Clinodactyly of the 5th finger;C4021085:Abnormal brain morphology Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Knight Diagnostic Laboratories, Oregon Health and Sciences University | Feb 22, 2019 | - - |
RBM8A-related disorder Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 20, 2024 | The RBM8A c.67+32G>C variant is predicted to interfere with splicing. The c.67+32G>C substitution is found in apparently unaffected individuals at frequencies over 0.5%. However, significant evidence suggests the c.67+32G>C substitution is a “functional polymorphism” and is likely a cause of disease only when paired with a null RBM8A allele, such as a large 1q21.1 deletion that encompasses the RBM8A gene. Large RBM8A deletions found in trans with a functional polymorphism such as c.67+32G>C have been identified in many patients with autosomal recessive thrombocytopenia with absent radius (TAR) (Albers et al. 2012. PubMed ID: 22366785; Boussion et al. 2020. PubMed ID: 32227665). Therefore, we consider this variant to be likely pathogenic. - |
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at