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