Some conflicting ClinVar interpretations could be displayed with better information about exomiser HOT 2 CLOSED

Added a new field and method Map<ClinSig, Integer> getConflictingInterpretationCounts() to the ClinVarData class and underlying protobuf representation in the new ClinVar MVStore (see #501). This allows display of the conflicting interpretation counts in the HTML e.g.

Previously:
MISSENSE_VARIANT SNV 13-110855918-C-G [0/1] rs150182714
Exomiser ACMG: UNCERTAIN_SIGNIFICANCE [PP3]
ClinVar: CONFLICTING_PATHOGENICITY_INTERPRETATIONS (criteria provided, conflicting interpretations)

Updated:
MISSENSE_VARIANT SNV 13-110855918-C-G [0/1] rs150182714
Exomiser ACMG: UNCERTAIN_SIGNIFICANCE [PP3]
ClinVar: CONFLICTING_PATHOGENICITY_INTERPRETATIONS (criteria provided, conflicting interpretations) (VUS:1, LB:3)

from exomiser.

You're in luck - I'm working on updating some of the ClinVar stuff right now. Also, as luck would have it the ClinVar VCF file has the following INFO field

##INFO=<ID=CLNSIGCONF,Number=.,Type=String,Description="Conflicting clinical significance for this single variant; multiple values are separated by a vertical bar">

which appears when CLNSIG/CLNREVSTAT list conflicting interpretations e.g. (trimming out unwanted fields)

1       930200  1043045 G       A       .       .       CLNREVSTAT=criteria_provided,_conflicting_interpretations;CLNSIG=Conflicting_interpretations_of_pathogenicity;CLNSIGCONF=Uncertain_significance(1)|Likely_benign(1);
1       930201  2012623 C       T       .       .       CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;
1       930203  972363  C       T       .       .       CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Uncertain_significance

So, yes. This is a good idea and not so hard to achieve. I'd originally though this would require collating all this from the XML dump which would have led to a more negative response!

from exomiser.