Variants can be stated by using transcript-dependant cDNA and/or protein coordinates by using HGVS syntax and/or genomic coordinates in the GRCh19/hg37 build (see more details below). To pass genomic coordinates in other assembly versions, use the option of uploading a VCF file or consider using conversion tools.

The system will check for annotation consistency and convert the variants to left-aligned genomic coordinates as required for the variant analyses performed by the public version of the MTBP. In case that any problem occurs during the variant re-mapping, the system will raise the corresponding warning and will not proceed with the analysis.

Protein coordinates

The variant definition must include the sequence identifier and the protein change following the HGVS syntax. The public MTB portal accepts three-letter amino acid codes as well as one-letter abbreviations (e.g. p.Val600Glu or p.V600E). The public MTBP portal accepts transcript and protein identifiers from both EBI (e.g. ENST00000288602.6 or ENSP00000288602.6) and NCBI (e.g. NM_004333.4 or NP_004324.4) systems. If this information is not available, the portal also accepts the use of a valid HGNC symbol (e.g. BRAF). In the latter case, the system will try to infer the transcript that is consistent with the protein change stated for the variant, as this information is needed for the variant interpretation. See some examples below:

Amino acid change: NRAS:p.Q61L

Stop codon insertion: PTEN:p.R233*

Inframe insertion: AATK:p.P1331_A1332insTP

Inframe deletion: AADACL4:p.W263_I267delWRDAI

Inframe del plus insertion: TSC1:p.N198_F199delinsI

Frameshift: BRCA1:p.S1330Rfs*5

cDNA coordinates

The variant definition must include the sequence identifier and the cDNA change following the HGVS syntax. The portal accepts transcript and protein identifiers from both EBI (e.g. ENST00000288602.6 or ENSP00000288602.6) and NCBI (e.g. NM_004333.4 or NP_004324.4) systems. If this information is not available, the portal also accepts the use of a valid HGNC symbol (e.g. BRAF). In the latter case, the system will try to infer the transcript that is consistent with the cDNA change stated for the variant, as this information is needed for the variant interpretation. See some examples below:

Substitution of a nucleotide: CHEK1:c.207A>C

Insertion of a single nucleotide: VHL:c.477_478insC

Insertion of several nucleotides: EGFR:c.2310_2311insGGTACA

Deletion of a single nucleotide: FAM175A:c.908delA

Deletion of several nucleotides: PALB2:c.172_175delTTG

Insertion and deletion of several nucleotides: MRE11A:c.592_593delGTinsTA

Genomic coordinates

The variant definition must include the chromosome number, the genomic coordinates (in GRCh37/hg19 build) and the reference and variant nucleotides (in the ‘+’ strand). See some examples below:

Substitution of a nucleotide: chr3:g.52437215C>T

Insertion of a single nucleotide: chr17:g.37880991_37880992insC

Insertion of several nucleotides: chr3:g.10188243_10188244insAGA

Deletion of a single nucleotide: chr8:g.90965676delT

Deletion of several nucleotides: chr13:g.32903583_32903584delGA

Insertion plus deletion: chr7:g.140453136_140453137delACinsTT

Copy number alterations

Copy number alterations are stated at the gene level using the gene symbol plus the tags "AMP" and "DEL" to indicate gain or loss in the number of gene copies, respectively. Note that the system assumes that the alteration is unequivocal and that the number of copies gained or lost is significant. Examples listed below:

• TP53:DEL
• BRCA1:DEL
• ERBB2:AMP
• FGFR1:AMP

Note that the system assumes that the alteration is unequivocal and that the number of copies gained or lost is significant.

Gene fusions

Gene fusions can be stated by using both partners (separated by a "-") or only the cancer gene partner plus the tag "FUS". Note that the system assumes that the fusion is unequivocal. Examples listed below:

• BCR-ABL1:FUS
• PCM1-JAK2:FUS
• FGFR2:FUS
• NTRK1:FUS