Examples

dbSNP rs id (rsNNN...N)

Single Nucleotide Variants (SNVs): rs145236923, rs117260922rs376932266,  rs113488022,  rs1421085 

Insertions: rs361923,  rs150781976

Deletions: rs371997714,  rs66698963


HGVS DNA-level variants

SNVs: GALNT12:c.907G>ASORL1:c.808G>ABRAF:c.1799T>GTP53:c.559G>A

FTO:c.46-43098T>C (or NM_001080432:c.46-43098T>C or ENST00000471389:c.46-43098T>C or NM_001080432(FTO):c.46-43098T>C)

Insertions: SYNGR1:c.607_608insACA, BRCA1:c.69_70insA

Deletions: BAIAP2L2:c.1322_1363delFADS2:c.208-2713_208-2692del

Subtitutions: TYR:c.1205_1206delGAinsAT

Duplications: BRCA1:c.64_65dupTT


Single amino acid variants

GALNT12 D303N or GALNT12 p.Asp303Asn

TP53:R175L or NM_000546.5(TP53):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 or ENST00000268057:I354T

NPPA:*152RTP53:G187SPIK3CA:H1047R


chromosome—position—ref seq—variant seq

Delimiters: any combination of spaces, dashes (-) and colons (:), chromosomes starting with 'chr' or without

SNPs: 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-AchrX: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)

           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


Genomic Position

5:156479558 (or chr5-156479558)


Gene Symbol

BRAF, EGFR, BRCA1


Transcript Identifier

NM_002482.3

ENST00000288602

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