User: cocchi.e89

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cocchi.e8910
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Posts by cocchi.e89

<prev • 20 results • page 1 of 2 • next >
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variant REF-ALT conversion to HGVS.c
... Dear all, I am quite new so sorry if this is a silly question. I am working on a VCF files and comparing my variant with GnomAD DB. I noticed that the VEP column of Gnomad HGVS.c bases are different from the REF-ALT bases. As example, GnomAD DB row: *21 10944679 rs770820681 **C A** 3696.48 RF AC= ...
gene hgvs nomeclature variants written 1 hour ago by cocchi.e8910 • updated 36 minutes ago by Pierre Lindenbaum118k
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VARIANT effect retrieving
... Dear all, I am working on a database of several patients with relative variants (SNV and INDELS basically) VCF files. I know I can check for variant effect against VEP DB or similar, but for variants that are absent in such databases, how can I possibly categorize them in effect result? (e.g. missen ...
indel variant effect snv written 1 day ago by cocchi.e8910
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Comment: C: Variant Effect Prediction Databases
... basically SNV/INDEL in exome studies, but I would appreciate so much even broader comments ...
written 6 days ago by cocchi.e8910
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Variant Effect Prediction Databases
... Dear all, I have to find the predicted effect of a large sample of variants, I know about GnomAD VEP annotation but some of them are absent in GnomAD. How could I try to retrieve those variants effect? Other Databases etc? PS: I have to integrate it into a pipeline so I need some source database, ...
variant database prediction effect written 8 days ago by cocchi.e8910
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Comment: C: all non-ALT position in a VCF are non-variants?
... Thanks for confirming! ...
written 9 days ago by cocchi.e8910
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all non-ALT position in a VCF are non-variants?
... Dear all, it is a silly question but I have to make extremely sure about an analysis that I am doing. In a VCF file, all positions with NO ALT allele are considered as NON-VARIANT right? ex. 'CHROM': 'chr1', 'POS': '1243983', 'ID': '.', 'REF': 'G', 'ALT': '.', 'QUAL': '.', 'FILTER': 'OffTarget ...
vcf altered alt variant written 9 days ago by cocchi.e8910 • updated 9 days ago by Pierre Lindenbaum118k
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Comment: C: CLINVAR multiple molecular consequences
... Sorry cpad, I don’t get you, do you mean that this specific mutation results in 4 different consequences depending on the gene splice variant transcript? Or are you pointing out something else? ...
written 6 weeks ago by cocchi.e8910
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CLINVAR multiple molecular consequences
... Dear all, I've noticed that in CLINVAR multiple "molecular consequences" are showed for each variant, as example: https://www.ncbi.nlm.nih.gov/clinvar/variation/221294/ is indicated as: NM_020771.3(HACE1):c.454C>T (p.Gln152Ter) but in the section molecular consequence 4 different variants are s ...
effect clinvar variant molecular consequence written 6 weeks ago by cocchi.e8910
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clinvar "Affects" meaning
... Dear all, what exactly clinker CLNSIG "Affects" stands for? I couldn't exactly figured it out... Thanks a lot in advance for any help ...
clinvar meaning affects written 6 weeks ago by cocchi.e8910
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Loss Of Function known affected genes
... Dear all, I’m trying to figure out if there is a rapid way to assess this point: the ACMG guidelines (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4544753/) for clinical interpretation of variants state: “*Null variant (nonsense, frameshift, canonical +/−1 or 2 splice sites, initiation codon, sing ...
variants lof clinical annotation acmg written 6 weeks ago by cocchi.e8910

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