Where can I find a database of healthy genotypes as well as a database of genetic diseases to link these data?

Question

[Crypto]

Hello. I have the results of decoding a genome consisting of approximately 600 thousand lines in a vcf file. I need to compare it with a database that would indicate a 'healthy genotype' regarding genetic diseases. And also compare the genotype with the base of genetic diseases. for exemple:

• healthy genotype for rs397507170 is GG

but

• genotype GA causes Biotinidase deficiency

What I did: I downloaded the database https://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz
I compared the data with the database and found that the database from 00-All.vcf.gz does not contain a healthy genotype. I also cannot understand what I can compare the 'RelatedGenes' column with in case of identifying an unhealthy genotype from here https://ftp.ncbi.nlm.nih.gov/pub/clinvar/gene_condition_source_id

This leads to two questions. the first one is where I can find a database with a healthy genotype, and also where I can find a database of genetic diseases to compare with the analysis result?

Answer 1

[Jeremy Leipzig]

There is a maxim in law that states if something isn't explicitly illegal, it's legal. The same principle likely holds true for biology.

So you will find known curated deleterious variants in clinvar.

You also will likely not see certain variants in gnomAD, because they are dominant penetrant deleterious variants. No offspring could survive it.

Others will be ultra-rare (<0.00002 allele frequency). If those are in genes they could be deleterious, or not.

No variant or reference will be labeled "healthy".