Comments (2)
ManavalanG
commented on August 19, 2024
After a bit more probing, this file has all ClinVar IDs with wrong gene mapping. Column 'symbol' was obtained from clinvar_alleles.single.b37.tsv.gz, and columns 'geneID_from_refseqID' and 'geneName_from_refseqID' were obtained using RefSeq ID associated with ClinVar IDs.
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simnim
commented on August 19, 2024
I just looked up the example you Highlighted.
At least for this case it's the same issue I raised earlier.
31
The first gene symbol in the xml file is C1orf167 and the second is MTHFR.
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Related Issues (20)
- Sometimes "symbol" disagrees with primary hgvs gene annotation HOT 1
- Missing variants HOT 4
- RScript crash HOT 1
- Feature request: Including strand info and genomic start and end coordinates HOT 1
- Add "last_evaluated" field to VCF
- Improper handling of pseudoautosomal region HOT 1
- Improper labelling of conflicting variants as pathogenic HOT 3
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- Add LICENSE HOT 2
- Need to Update pathogenic & conflict boolean regex. HOT 1
- ClinSig changes for some halpotypes in join_data.R - become wrong! HOT 2
- Clinical Significance Order Lost in Allele Grouping HOT 8
- Convert the pipeline to hail for .tsv processing steps?
- Augmented tables in output HOT 2
- missing clinvar_alleles_with_exac_v1.*.tsv.gz HOT 1
- Mismatch between clinical_significance_ordered and submitters_ordered HOT 2
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