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
In VarSome, CNVs are encoded in a colon separated, four field format:
<chromosome>:<start coordinate>:<L|E><end coordinate>:<DUP|DEL>
Field 1 - chromosome: chromosome in UCSC format, for example “chr1”, “chr9”, “chrX”, etc.
Field 2 - start coordinate: genomic coordinate denoting the start position of the CNV.
Field 3 - end coordinate/length: If preceded by “E” or “e” (end), the coordinate denotes the end position of the CNV. If preceded by an “L” or “l” (length), then it denotes the length of the CNV. If there is no preceding flag, then “E” is implied.
Field 4 - copy number variation type. Value can be “DUP” for duplications or “DEL” for deletions.
hg19 reference genome
chr7:117138367:117159446:DEL
A Pathogenic 21,079bp long deletion spanning exons 1 and 2 of CFTR
chr3:37039445:37059613:DUP
A 20,168 Likely Pathogenic duplication spanning exons 3-10 of MLH1
chr21:36160098:36171759:DEL
A 11,661 Pathogenic deletion spanning the final two exons of the RUNX1 transcript
chr1:110230496:110235917:DUP
A 5,421 Benign duplication spanning genes GSTM1 and GSTM2
chr2:97854824:97855027:DUP
A 203bp duplication of Uncertain Significance spanning parts of exons 33 and 34 of ANKRD3
hg38 reference genome
chr1:13308329:13308887:DEL
A 558bp Benign deletion of large part of exon 4 of PRAMEF4
chr13:32317656:32331987:DUP
A 4,331bp Likely Pathogenic duplication of exon 3 of BRCA2
8:127734450:127764981:DUP
A 30,531bp duplication of Uncertain Significance spanning MYC
chr1:13308329:13308887:DEL
A 558bp Benign deletion of large part of exon 4 of PRAMEF4
