Errors

[ekartsak]

On REF/ALT alleles

Source : VEP
rs758320086
rs72549351
rs730882170

Source : UCSC
rs3832694
rs72466463 [ has merged into rs587778873 ]
rs5030656
rs72549380
rs8175347 !!
rs3215983
rs28399445
rs267607275

Source : NC_transcript
NC_000022.11:g.42132048_42132049insTT
NC_000022.11:g.42132048_42132049insT
NC_000022.11:g.42132048_42132049delTT

[ekartsak]

After LiftOver : common offsets

Offset on GRCH38 -> (liftOver)Offset on GRCH37 : Variant(GRCH38) : Variant(GRCH37)
42126914 -> 42522916 : NC_000022.11:g.42126914C>G : rs149157808 C>T
42128217 -> 42524219 : NC_000022.11:g.42128217_42128218insG : rs148769737 G>T

rs148769737 in dbSNP appears to be biallelic. G>T, G>A
On our JSON file is only G>T according to UCSC

[ekartsak]

Duplicated Offsets that correspond to different variants

According to GRCH37
Offset : Gene : Variant : Source
41352258 : CYP2A6 : 4074delA : BLAT
41352258 : CYP2A6 : 4071delA : BLAT
41352954 : CYP2A6 : 3378C>T : BLAT
41352954 : CYP2A6 : 657C>T : BLAT
41354553 : CYP2A6 : 459G>A : BLAT
41354553 : CYP2A6 : 1779G>A : BLAT
41354851 : CYP2A6 : 1471_1476delCTCTCT : BLAT
41354851 : CYP2A6 : 1481_1486delCTCTCT : BLAT
234676941 : UGT1A1 : 1160(CC>GT) : BLAT
234676941 : UGT1A1 : 1159(C>T) : BLAT
153762634 : G6PD : 561_563delCTC : NC_transcript
153762634 : G6PD : rs5030868 : UCSC
153764234 : G6PD : 185C->A : NC_transcript
153764234 : G6PD : 185C->T/A : NC_transcript

rs72558184 doesn't map to any assembly
96535210 : CYP2C19 : rs72552267 : UCSC
96535210 : CYP2C9 : rs72558184 : NC_transcript

rs144041067 hgvs name : NM_000367.3:c.488G>A
18139200 : TPMT : NM_000367.2:c.488G>C : NC_transcript
18139200 : TPMT : rs144041067 : UCSC

From cypalleles rs4986909 is 22026C>T, which could be mistaken with 26206C>A?
99359670 : CYP3A4 : rs4986909 : UCSC
99359670 : CYP3A4 : 26206C>A : UCSC

The following seem to be biallelic but are reported as two different variants on json
41350615 : CYP2A6 : 5717C>G : BLAT
41350615 : CYP2A6 : 5717C>T : BLAT

234676506 : UGT1A1 : 1007(G>A) : BLAT
234676506 : UGT1A1 : 1007(G>T) : BLAT

According to GRCH38
Offset : Gene : Variant : Source
42522660 : CYP2D6 : NC_000022.11:g.42126658_42126666dupAGTGGGCAC : NC_transcript
42522660 : CYP2D6 : NC_000022.11:g.42126658A>G : NC_transcript

[ekartsak]

Update dbSNP version (current 142) : 08 January 2016 - dbSNP 144 Available for hg19 and hg38

variants appear to have 3 alternative alleles instead of 2 (errors probably due to the dbSNP version)
rs55886062
rs55752064
rs55640102
rs7900194
rs56165452
rs55901008
rs56387224
rs56199088
rs56240201
rs56107638
rs1799966
rs4986850
rs4986891
rs35303484
rs45482602
rs55989760
rs55771538
rs72549387
rs5030865
rs55918055
rs34059508
rs4986909
rs4986908
rs55951658
rs137852328

[kantale]

Insertion: rs1799752.
FIXED: 0a3a797

[kantale]

41352258 : CYP2A6 : 4074delA : BLAT
41352258 : CYP2A6 : 4071delA : BLAT

These are the same. http://www.cypalleles.ki.se/cyp2a6.htm https://mutalyzer.nl/name-checker?description=NG_008377.1%3Ag.9092delA

41352954 : CYP2A6 : 3378C>T : BLAT
41352954 : CYP2A6 : 657C>T : BLAT

NG_008377.1:g.8399C>T
NG_008377.1:c.657C>T

41354553 : CYP2A6 : 459G>A : BLAT
41354553 : CYP2A6 : 1779G>A : BLAT

NG_008377.1:c.459G>A
NG_008377.1:g.6800G>A

41354851 : CYP2A6 : 1471_1476delCTCTCT : BLAT
41354851 : CYP2A6 : 1481_1486delCTCTCT : BLAT

NG_008377.1:g.6502_6507delCTCTCT
NG_008377.1:g.6502_6507delCTCTCT
FIXED: 9d3299c