Table 2 Output tables for the TransAT package
(a) | Â | Â | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Transcript_version | Nucleotide_changes | CDS_start_loc | Ref | Alt | Chr | ensembl_transcript_id | hgnc_symbol | start | end | width | strand | exon_id | exon_rank | tx_start | tx_end | refsnp_id |
NM_005359 | A947G | 947 | A | G | 18 | ENST00000342988 | SMAD4 | 48,586,278 | 48,586,278 | 1 |  +  | ENSE00003494728 | 8 | 1485 | 1485 | rs377119288 |
NM_000059 | C3109T | 3109 | C | T | 13 | ENST00000544455 | BRCA2 | 32,911,601 | 32,911,601 | 1 |  +  | ENSE00000939168 | 11 | 3336 | 3336 | rs80358557 |
NM_000059 | A4599C | 4599 | A | C | 13 | ENST00000544455 | BRCA2 | 32,913,091 | 32,913,091 | 1 |  +  | ENSE00000939168 | 11 | 4826 | 4826 | rs80358694 |
(b) | Â | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
Chr | Start | End | Ref | Alt | gnomAD_exome _ALL_Ref_freq | gnomAD_exome _ALL_Alt_freq | gnomAD_exome _AFR_Ref_freq | gnomAD_exome _AFR_Alt_freq | gnomAD_exome _AMR_Ref_freq | gnomAD_exome _AMR_Alt_freq | gnomAD_exome _ASJ_Ref_freq | gnomAD_exome _ASJ_Alt_freq |
18 | 48,586,278 | 48,586,278 | A | G | 0.9999 | 1.00E−04 | 1 | 0 | 1 | 0 | 1 | 0 |
13 | 32,911,601 | 32,911,601 | C | T | 1 | 0 | 1 | 0 | 1 | 0 | 1 | 0 |
13 | 32,913,091 | 32,913,091 | A | C | 0.9999 | 1.00E−04 | 1 | 0 | 1 | 0 | 1 | 0 |
gnomAD_exome_EAS_Ref_freq | gnomAD_exome_EAS_Alt_freq | gnomAD_exome_FIN_Ref_freq | gnomAD_exome_FIN_Alt_freq | gnomAD_exome_NFE_Ref_freq | gnomAD_exome_NFE_Alt_freq | gnomAD_exome_SAS_Ref_freq | gnomAD_exome_SAS_Alt_freq | gnomAD_exome_OTH_Ref_freq | gnomAD_exome_OTH_Alt_freq |
|---|---|---|---|---|---|---|---|---|---|
0.9999 | 1.00E−04 | 1 | 0 | 1 | 0 | 0.9997 | 3.00E-04 | 1 | 0 |
0.9999 | 1.00E−04 | 1 | 0 | 1 | 0 | 1 | 0 | 1 | 0 |
0.9987 | 0.0013 | 1 | 0 | 1 | 0 | 1 | 0 | 1 | 0 |
Func.knownGene | Gene.knownGene | ExonicFunc.knownGene | AAChange.knownGene |
|---|---|---|---|
exonic | SMAD4 | nonsynonymous SNV | SMAD4:uc002lfb.4:exon4:c.A482G:p.N161S,SMAD4:uc010xdp.2:exon8:c.A947G:p.N316S |
exonic | BRCA2 | stopgain | BRCA2:uc001uub.1:exon11:c.C3109T:p.Q1037X |
exonic | BRCA2 | nonsynonymous SNV | BRCA2:uc001uub.1:exon11:c.A4599C:p.K1533N |