rs746753722
NM_017882.3(CLN6):c.679G>A
SYNGR1:c.607_608insACA
BRAF:V600E
5:156479558:15:
7-151945072--T
5:156479558
BRAF
NM_002482
chr2:47630263:47639699:DEL
AGTCCRAGTTGTAAATGGTACACTCGGCGTAAGCCTGAAAAGATAAAATCAAAGATGTAAAGGTGAGCACAGTCTAAGTTCTCTCTGAAGTGTCAATGGGAATGCAGATTGGATTAAATAAATGCTGCCCAAGTGCATACTCAAAGAGGC

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Formats accepted for variant, gene, transcript, position and region queries

dbSNP rs id (rsNNN...N)

Single Nucleotide Variants (SNVs): rs746753722rs145236923, rs117260922rs376932266,  rs113488022,  rs1421085 

Insertions: rs361923,  rs35104581

Deletions:  rs66500630,  rs66698963


HGVS DNA-level variants

SNVs: CLN6(NM_017882):c.679G>AGALNT12:c.907G>ASORL1:c.808G>ABRAF:c.1799T>GTP53: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_1363delFADS2: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

CLN6 E227K or CLN6 Glu227Lys

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:*152RTP53:G187SPIK3CA: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:A:T (or chr15-68500735-A-T)

           15-73027478-T-C (or chr15:73027478:T:C or chr15 73027478 T C)

           chr6-161127501-T-G (or 6:161127501:T:G or 6 161127501 T G)

          11-89017961-T-AchrX:138643751:A:T

Insertion: chr22:39777823::CAA (or 22-39777823--CAA or chr22-39777823-T-CCAA)

Deletion: 5:156479558:TAAAGCACTAAGACC: (or chr5:156479558:TAAAGCACTAAGACC:)


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)

           11-89017961-1-A

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

chr2  45944181  . AAGATGAGATGAGAT AAGATGAGAT  12.7101 FAIL  AC1=2;AF1=1;DP=1;DP4=0,0,0,1;FQ=-37.5258;IDV=1;IMF=1;INDEL;MQ=50;MQ0F=0;SGB=-0.379885 GT:PL 1/1:50,3,0


COSMIC id

COSV54347687COSM4986760


Transcript or genomic position

HAVCR1:c.487 or 5:156479558 or chr5-156479558


Genomic region

chr5:156479372..156479666


Gene symbol or identifier

BRAF, EGFR, BRCA1

HGNC:1097, ENTREZ:1956, UNIPROT:B7ZA85


Transcript identifier

NM_002482

ENST00000586385

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