Splice Site Frequency/ Pathogenicity Data

Question

[Parth Patel]

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

Answer 1

[Emily]

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.

[EnsemblWill]

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