dbSNP Queries

Query rsID via myvariant.info

import myvariant

mv = myvariant.MyVariantInfo()

def get_rsid_info(rsid): '''Get variant info by rsID''' result = mv.getvariant(rsid, fields=['dbsnp', 'clinvar', 'gnomad_exome']) return result

result = get_rsid_info('rs121913527')

Query via NCBI Entrez

from Bio import Entrez import xml.etree.ElementTree as ET

Entrez.email = 'your@email.com'

def search_dbsnp(rsid): '''Search dbSNP by rsID''' handle = Entrez.esearch(db='snp', term=rsid) record = Entrez.read(handle) handle.close() return record

def fetch_dbsnp(snp_id): '''Fetch dbSNP record by internal ID''' handle = Entrez.efetch(db='snp', id=snp_id, rettype='xml') xml_data = handle.read() handle.close() return xml_data

Map Coordinates to rsID

def coords_to_rsid(chrom, pos, ref, alt): '''Find rsID for genomic coordinates''' mv = myvariant.MyVariantInfo()

# Query by HGVS notation
hgvs = f'chr{chrom}:g.{pos}{ref}>{alt}'
result = mv.getvariant(hgvs, fields=['dbsnp.rsid'])

if result:
    return result.get('dbsnp', {}).get('rsid')
return None

Map rsID to Coordinates

def rsid_to_coords(rsid): '''Get genomic coordinates for rsID''' mv = myvariant.MyVariantInfo() result = mv.getvariant(rsid, fields=['dbsnp', 'vcf'])

if not result:
    return None

dbsnp = result.get('dbsnp', {})
return {
    'chrom': dbsnp.get('chrom'),
    'pos': dbsnp.get('hg38', {}).get('start'),
    'ref': dbsnp.get('ref'),
    'alt': dbsnp.get('alt')
}

Batch rsID Lookup

def batch_rsid_lookup(rsids, fields=None): '''Look up multiple rsIDs''' mv = myvariant.MyVariantInfo()

if fields is None:
    fields = ['dbsnp', 'clinvar.clinical_significance', 'gnomad_exome.af.af']

results = mv.getvariants(rsids, fields=fields)
return results

Parse dbSNP Annotations

def parse_dbsnp(result): '''Extract key dbSNP annotations''' dbsnp = result.get('dbsnp', {})

return {
    'rsid': dbsnp.get('rsid'),
    'chrom': dbsnp.get('chrom'),
    'pos_hg38': dbsnp.get('hg38', {}).get('start'),
    'pos_hg19': dbsnp.get('hg19', {}).get('start'),
    'ref': dbsnp.get('ref'),
    'alt': dbsnp.get('alt'),
    'gene': dbsnp.get('gene', {}).get('symbol'),
    'class': dbsnp.get('class'),  # snv, ins, del, etc.
    'validated': dbsnp.get('validated')
}

Variant Classes in dbSNP

Class Description

snv Single nucleotide variant

ins Insertion

del Deletion

indel Insertion/deletion

mnv Multiple nucleotide variant

Query NCBI Variation Services API

import requests

def query_spdi(rsid): '''Query NCBI Variation Services for SPDI notation''' url = f'https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid[2:]}' response = requests.get(url) if response.ok: return response.json() return None

Related Skills

• myvariant-queries - Aggregated variant queries

• clinvar-lookup - ClinVar pathogenicity

• database-access/entrez-search - General Entrez queries