Discrepancy between the downloaded clinvar, dbNSFP and website

Question

[MAPK2]

Hi All, I encountered discrepancies in clinvar annotations, leading to inconsistencies:

1. Discrepancies between locally downloaded datasets from clinvar and dbNSFP_CLINSIG and their respective web versions were noted. For instance, the variant (chr2:21006288:C:A) was labeled as Pathogenic in the downloaded datasets but not in the clinvar website. Conversely, chr2:21006288:C:T was marked as Conflicting_interpretations_of_pathogenicity in the downloaded datasets but deemed pathogenic on the clinvar website.

2. Variants also exhibited discordance between the downloaded clinvar and dbNSFP_CLINSIG datasets, even though they were based on the same version.

Can someone please help me understand why this issue?

[Ram]

What are the versions of the downloaded dataset and the one online?

[MAPK2]

The one downloaded was from 2022-04-30 for both dbNSFP and Clinvar. Web version is from 2023 (https://www.ncbi.nlm.nih.gov/clinvar/variation/17890/#id_second)

[Ram]

Look for additional pieces of evidence submitted in the time between - they're the reason you see a different CLINSIG value.

[GenoMax]

If you are certain about the discrepancy then reach out to clinvar support at clinvar at ncbi.nlm.nih.gov