Known databases for pathogenic SNV's in the non coding regions

Question

[osiemen]

Is there any database available for known pathogenic non coding SNV's ?

I want to use it for validation.

All tips are welcome!

Answer 1

[Pierre Lindenbaum]

A rough exploration using NCBI Clinvar and my tool xsltstream: http://lindenb.github.io/jvarkit/XsltStream.html

invoke:

$ curl -s  "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_00-latest.xml.gz" | gunzip -c |\
   java -jar dist/xsltstream.jar  -t transform.xsl -n ClinVarSet

output:

RCV000203227	
RCV000256194	
RCV000256207	
RCV000000913	
RCV000000914	
RCV000006518	
RCV000015276	
RCV000015277	
RCV000015291	
RCV000015295	
RCV000023096	
RCV000023097	
RCV000023099	
RCV000023100	
RCV000023101	
RCV000023102	
RCV000032637	
RCV000032638	
RCV000202309	
RCV000202310	
RCV000202311	
RCV000202312	
RCV000202313	
RCV000202314	
RCV000202315	
RCV000412610	
RCV000169492	
RCV000007746	
RCV000007748	
RCV000007749	
RCV000007750	
RCV000007751	
RCV000031168	
RCV000031230	
RCV000077142	
RCV000083054	
RCV000112217	
RCV000112319	
RCV000112372	
RCV000112463	
RCV000112468	
RCV000112754	
RCV000254920	
RCV000255241	
RCV000313899	
RCV000370918	
RCV000007747
RCV000007744	
RCV000007745	
RCV000015275	
RCV000020067	
RCV000023192	
RCV000032556	
RCV000032558	
RCV000032559	
RCV000032560	
RCV000032561	
RCV000032562	
RCV000032563	
RCV000032564	
RCV000032565	
RCV000032567	
RCV000032568	
RCV000032569	
RCV000032570	
RCV000032571	
RCV000032572	
RCV000032573	
RCV000032574	
RCV000032575	
RCV000032576	
RCV000032577	
RCV000032579	
RCV000032580	
RCV000032581	
RCV000032582	
RCV000032583	
RCV000032584	

view raw README.md hosted with ❤ by GitHub

	<?xml version="1.0" encoding="UTF-8"?>
	<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns="http://www.w3.org/1999/xhtml">
	<xsl:output method="text"/>
	<xsl:template match="/"><xsl:apply-templates/></xsl:template>
	<xsl:template match="ReleaseSet"><xsl:apply-templates/></xsl:template>
	<xsl:template match="ClinVarSet">
	<xsl:if test="count(.//Attribute[@Type='MolecularConsequence'])=1">
	<xsl:variable name="csq" select=".//Attribute[@Type='MolecularConsequence']/text()"/>
	<xsl:if test="($csq = 'non-coding transcript variant' or $csq = 'intergenic variant' or $csq = '2kb upstream variant' or $csq = '5 prime utr variant' ) and .//Description[contains(text(),'athogenic')]">
	<xsl:value-of select="ReferenceClinVarAssertion/ClinVarAccession/@Acc"/>
	<xsl:text>
	</xsl:text>
	</xsl:if>
	</xsl:if>
	</xsl:template>
	</xsl:stylesheet>

view raw transform.xsl hosted with ❤ by GitHub

[osiemen]

thanks a lot dear Pierre!

[osiemen]

is there any chance to get the output in a Bed file format, i am interested in the positions of the mutations