Splice Site Frequency/ Pathogenicity Data
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6.6 years ago
Parth Patel ▴ 50

Hello, 

I need a data set that includes the frequency and pathogenicity labels for splice site mutations. I have tried to select these features from dbSNP, ClinVar, ESP, and PhenCode data sets I queried via EnsemblBioMart, but none of them actually contain frequency / pathogenicity labels. Any ideas where else to look? I cannot afford a 5k subscription to HGMD pro!

Thank you,

Parth

splice NNSplice Pathogenicity Ensembl BioMart • 1.7k views
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Entering edit mode
6.6 years ago

You should be able to get the minor allele frequency and the clinical significance from BioMart.

In this query I've filtered by consequence, choosing all the splice-site related ones. Then I've picked the 1000 Genomes MAF, clinical significance as well as some phenotype stuff as attributes.

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BioMart sometimes doesn't work well with genome-wide queries such as this.

You could grep our VCF dump files; this command finds variants with any clinical significance states that are splice-site related:

curl -s ftp://ftp.ensembl.org/pub/release-79/variation/vcf/homo_sapiens/Homo_sapiens_incl_consequences.vcf.gz | gzip -dc | grep CLIN | grep splic | less
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