Examples
Full Search
Search for anything in the VarSome database.
Examples: macular degeneration, "royal disease", article fish eye
Formats accepted for variant, gene, transcript, position and region queries
dbSNP rs id (rsNNN...N)
Single Nucleotide Variants (SNVs): rs746753722, rs145236923, rs117260922, rs376932266, rs113488022, rs1421085
Insertions: rs361923, rs35104581
Deletions: rs66500630, rs66698963
HGVS DNA-level variants
SNVs: CLN6(NM_017882):c.679G>A, GALNT12:c.907G>A, SORL1:c.808G>A, BRAF:c.1799T>G, TP53:c.559G>A
FTO:c.46-43098T>C (or NM_001080432:c.46-43098T>C οr FTO(NM_001080432):c.46-43098T>C)
Insertions: SYNGR1:c.607_608insACA, BRCA1:c.69_70insA (Note: "SYNGR1:c.607_608ins3" is not accepted)
Deletions: BAIAP2L2:c.1322_1363del, FADS2:c.208-2713_208-2692del (Note: "NM_004006:c.1147_1149delGAG" is accepted but "NM_004006:c.1147_1149del3" is not)
Subtitutions: TYR:c.1205_1206delGAinsAT or TYR:c.1205_1206delinsAT
Duplications: BRCA1:c.64_65dupTT
HGVS single amino acid substitutions
GALNT12 D303N or GALNT12 p.Asp303Asn
TP53:R175L or TP53(NM_000546):R175L or NM_000546:R175L
BRAF:V600E or BRAF:p.V600E or BRAF:p.Val600Glu
BBS4:I354T or BBS4:p.Ile354Thr or NM_033028:I354T
NPPA:*152R, TP53:G187S, PIK3CA:H1047R
Note: We do not accept protein insertions, deletions or frameshift variants, since they usually cannot be mapped to one or a few alternative genomic variants. All protein variants are converted into genomic variants, and only those affecting a single codon are considered; therefore a single amino acid subscritution coming from alterations to more than one codon, or one that truncates the protein may not be mapped from your query to all possible genomic variants giving rise to it.
chromosome—position—ref seq—variant seq
Delimiters: any combination of spaces, dashes (-) and colons (:), chromosomes starting with 'chr' or without
SNPs: 15:68500735:C:T (or chr15-68500735-C-T)
15-73027478-T-C (or chr15:73027478:T:C or chr15 73027478 T C)
chr6-161127501-A-G (or 6:161127501:A:G or 6 161127501 A G)
11-89017961-G-A, chrX:138643751:C:T
Insertion: chr22:39777823::CAA (or 22-39777823--CAA or chr22-39777822-C-CCAA)
Deletion: 5:156479558:TTGGAACAGTCGTCA: (or chr5-156479558-TTGGAACAGTCGTCA:)
chromosome—position—ref_seq_length—variant_seq
ref_seq_length: number of reference bases that the variant allele replaces
SNP ('1' as third place):
15-73027478-1-C (or chr15:73027478:1:C or 15 73027478 1 C)
chr6-161127501-1-G (or 6:161127501:1:G or 6 161127501 1 G)
Insertion ('0' as third place):
22:39777823:0:CAA (or chr22:39777823-0-CAA or chr22 39777823 0 CAA)
Deletion (number of bp deleted in third place):
chr22:38482353:42: or 22-38482353-42- or 22 38482353 42
Line from your VCF
COSMIC id
Transcript or genomic position
HAVCR1:c.487 or 5:156479558 or chr5-156479558
Genomic region
Gene symbol or identifier
HGNC:1097, ENTREZ:1956, UNIPROT:B7ZA85
Transcript identifier
CNVs
hg19 reference genome
chr7:117138367:117159446:DEL
A Pathogenic 21,079bp long deletion spanning exons 1 and 2 of CFTR
hg38 reference genome
chr1:13308329:13308887:DEL
A 558bp Benign deletion of large part of exon 4 of PRAMEF4
