Question: SNP listed on dbSNP website but not in VCF
gravatar for jfjiang
5.6 years ago by
jfjiang10 wrote:

Hi all,

I am dealing with couple of SNPs, however, I found several SNPs are indeed listed on the dbSNP website, but not listed in the dbSNP VCF file from the ftp server.

For example, rs1265181:, according to this website, it should be presented in 144 build, but it turns out NULL when I grep this SNP in 144 GRCh37.p13 or GRCh38.p2 build vcf file.


Could any one give me some suggestions on how to get a full list for this issue?


snp • 2.3k views
ADD COMMENTlink modified 4.9 years ago by Biostar ♦♦ 20 • written 5.6 years ago by jfjiang10

I did search on b144 for both b38 and b37. Neither rsid and nor any variant at that reported position is present in both the VCFs.  You seem to be correct and you may have to contact NCBI/dbSNP maintainers regarding this discrepancy.

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by cpad011215k
On July 17th 2015 I observed a similar issue that I reported to NCBI Helpdesk: "I am wondering why the following pathogenic ALK variant is not present in the VCF file downloaded from here (downloaded July 17th, 2015):" This was the reply: "Thanks for reporting this to us. I have confirmed your report. Doubling checking this against the All_#.vcf.gz file for b144 mapped to GRCh37 and 38, I also see that this rsID is in those two vcf files. I will check with our developers to ask them looking into this issue.Thanks for reporting this to us." So there are definitely SNPs missing from some VCF files. I have not heard back from NCBI since, so I don't know if the problem persists.
ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Christian3.0k

I'm having the same issue. In fact I did a count of all the SNPs on chromosome 22 in the dbSNP BED format files and then did the same for the VCF file and found that there are +/-50 000 SNPs missing from the VCF file on chromosome 22 alone. @Christian Did you ever hear back from the NCBI help desk?

ADD REPLYlink written 5.3 years ago by davidbrownza0
No not yet. It strikes me that this issue still persists after 4 months.
ADD REPLYlink written 5.3 years ago by Christian3.0k
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