How to get REF/ALT allele for a list of rsid and SNP notations

Question

[Meisam]

I got an incomplete list of variants from an old study with only some rsids or coordinations, see example below:

Variant	Coordination
rs1585453	11:46884713
10:105087598_AT_A	10:105087598
rs145158522	10:106629859
rs180940	10:115722411
11:47277086_CTTTCTTTT_C	11:47277086

...

Now for my subsequent analysis I need to convert this to a standard VCF format table, with reference and alternate alleles information. I have searched online and have found a few ways I can do this like downloading the dbSNP big reference file which is not currently possible for me, and also using biomaRt it can only bring me back one single "allele" column which has all the possible variations for that SNP and also does not indicate which one is the reference:

snp_mart <- useEnsembl(biomart = "snp", dataset = "hsapiens_snp")

snp_info <- getBM(
   attributes = c("refsnp_id", "chr_name", "chrom_start", "chrom_end", "chrom_strand", "allele"),
   filters = "snp_filter",
   values = candidate_variant_id,
   mart = snp_mart

output example:

refsnp_id	chr_name	chrom_start	chrom_end	chrom_strand	allele
rs583104	109278685	109278685	G/A/C/T
rs599839	109279544	109279544	G/C/T

...

It seems like a trivial problem but I have had very hard time to find a simple and efficient way (preferably by doing an online query and not downloading gigabytes of data) to find the REF and ALT allele information for the rsid list, any help is very much appreciated. Thanks!

[GenoMax]

This may not be the best solution so I am going to leave it as a comment. But it is at least one solution.

Using EntrezDirect:

$ esearch -db snp -query "rs599839" | efetch -format docsum | xtract -pattern DocumentSummary -element DOCSUM | uniq
HGVS=NC_000001.11:g.109279544G>A,NC_000001.11:g.109279544G>C,NC_000001.11:g.109279544G>T,NC_000001.10:g.109822166G>A,NC_000001.10:g.109822166G>C,NC_000001.10:g.109822166G>T|SEQ=[G/A/C/T]|LEN=1|GENE=PSRC1:84722

$ esearch -db snp -query "rs583104" | efetch -format docsum | xtract -pattern DocumentSummary -element DOCSUM | uniq
HGVS=NC_000001.11:g.109278685G>A,NC_000001.11:g.109278685G>C,NC_000001.11:g.109278685G>T,NC_000001.10:g.109821307G>A,NC_000001.10:g.109821307G>C,NC_000001.10:g.109821307G>T|SEQ=[G/A/C/T]|LEN=1