Variants with conflicting interpretations studied for HSPG2-related disorder

Minimum review status of the submission for HSPG2-related disorder:		Collection method of the submission for HSPG2-related disorder:
Minimum review status of the other submission:		Collection method of the other submission:
Minimum conflict level: Report conflict between different conditions
Show significances as they were submitted (without aggregation into standard terms)

If a variant has more than two submissions, it may have multiple conflicts and therefore be counted in more than one conflict column. If this is the case, the "Variants with any kind of conflict" cell will be less than the sum of the conflicted variants cells to its left.

Variants with only 1 submission per condition	Variants with at least 2 submissions on the same condition and no conflicts	Variants with a synonymous conflict (e.g. benign vs non-pathogenic)	Variants with a confidence conflict (e.g. benign vs likely benign)	Variants with a benign or likely benign vs uncertain conflict	Variants with a category conflict (e.g. benign vs affects)	Variants with a clinically significant conflict (e.g. benign vs pathogenic)	Variants with any conflict
12	36	0	47	33	0	0	69

Significance breakdown #

In the table below, cells that correspond to a term paired with itself represent synonymous conflicts, i.e. variants that have been annotated with different terms that map to the same standard term. To compare the terms that were actually submitted, check the box in the filters section at the top of this page.

	All conditions
HSPG2-related disorder		pathogenic	uncertain significance	likely benign	benign
	likely pathogenic	2	0	0	0
	uncertain significance	0	0	2	0
	likely benign	0	29	0	31
	benign	0	2	14	0

Condition to condition summary #

Total conditions: 2

Download table as spreadsheet

Condition	Variants with only 1 submission per condition	Variants with at least 2 submissions on the same condition and no conflicts	Variants with a synonymous conflict (e.g. benign vs non-pathogenic)	Variants with a confidence conflict (e.g. benign vs likely benign)	Variants with a benign or likely benign vs uncertain conflict	Variants with a category conflict (e.g. benign vs affects)	Variants with a clinically significant conflict (e.g. benign vs pathogenic)	Variants with any conflict
not provided	0	37	0	42	33	0	0	68
not specified	0	26	0	16	4	0	0	18

All variants with conflicting interpretations #

Total variants: 69

Download table as spreadsheet

HGVS	dbSNP	gnomAD frequency
NM_005529.7(HSPG2):c.1167C>T (p.Asp389=)	rs145101074	0.00852
NM_005529.7(HSPG2):c.5755C>T (p.Arg1919Cys)	rs2229474	0.00657
NM_005529.7(HSPG2):c.12004C>G (p.Leu4002Val)	rs140403186	0.00485
NM_005529.7(HSPG2):c.4132G>A (p.Glu1378Lys)	rs62642525	0.00406
NM_005529.7(HSPG2):c.1082C>A (p.Thr361Asn)	rs75467696	0.00357
NM_005529.7(HSPG2):c.10498G>A (p.Val3500Met)	rs143543800	0.00313
NM_005529.7(HSPG2):c.13088C>T (p.Ser4363Leu)	rs62642502	0.00312
NM_005529.7(HSPG2):c.10937G>A (p.Arg3646His)	rs112062179	0.00305
NM_005529.7(HSPG2):c.4877G>A (p.Arg1626His)	rs41311989	0.00283
NM_005529.7(HSPG2):c.12982G>A (p.Ala4328Thr)	rs114015043	0.00254
NM_005529.7(HSPG2):c.7511G>A (p.Arg2504His)	rs62642517	0.00248
NM_005529.7(HSPG2):c.10677C>T (p.Asn3559=)	rs138049720	0.00243
NM_005529.7(HSPG2):c.10110G>A (p.Lys3370=)	rs141963344	0.00237
NM_005529.7(HSPG2):c.7191G>A (p.Ala2397=)	rs2290499	0.00219
NM_005529.7(HSPG2):c.3889-10G>A	rs147334960	0.00211
NM_005529.7(HSPG2):c.1238G>A (p.Arg413Gln)	rs140621959	0.00199
NM_005529.7(HSPG2):c.4489T>A (p.Phe1497Ile)	rs138460117	0.00171
NM_005529.7(HSPG2):c.4916C>T (p.Thr1639Met)	rs142433309	0.00171
NM_005529.7(HSPG2):c.12874G>A (p.Glu4292Lys)	rs141280063	0.00135
NM_005529.7(HSPG2):c.204C>A (p.Asp68Glu)	rs1869780	0.00131
NM_005529.7(HSPG2):c.4601C>G (p.Pro1534Arg)	rs142736845	0.00129
NM_005529.7(HSPG2):c.10280G>A (p.Arg3427Gln)	rs142939330	0.00120
NM_005529.7(HSPG2):c.12842G>A (p.Arg4281His)	rs151184052	0.00118
NM_005529.7(HSPG2):c.10204G>C (p.Val3402Leu)	rs150666616	0.00105
NM_005529.7(HSPG2):c.13018G>A (p.Val4340Met)	rs145687082	0.00103
NM_005529.7(HSPG2):c.7096G>A (p.Gly2366Arg)	rs140476180	0.00096
NM_005529.7(HSPG2):c.12580G>A (p.Gly4194Arg)	rs144496753	0.00088
NM_005529.7(HSPG2):c.11827G>A (p.Ala3943Thr)	rs116630187	0.00087
NM_005529.7(HSPG2):c.10917C>T (p.Tyr3639=)	rs111558823	0.00084
NM_005529.7(HSPG2):c.8381G>A (p.Arg2794Gln)	rs141563188	0.00084
NM_005529.7(HSPG2):c.8325C>T (p.Gly2775=)	rs142011049	0.00081
NM_005529.7(HSPG2):c.5648C>T (p.Ala1883Val)	rs140954748	0.00078
NM_005529.7(HSPG2):c.13145C>A (p.Ala4382Asp)	rs116316900	0.00076
NM_005529.7(HSPG2):c.4568G>A (p.Arg1523His)	rs147633715	0.00075
NM_005529.7(HSPG2):c.11072C>T (p.Thr3691Ile)	rs149159881	0.00066
NM_005529.7(HSPG2):c.9564G>C (p.Gln3188His)	rs149644947	0.00060
NM_005529.7(HSPG2):c.3708G>A (p.Ala1236=)	rs202214491	0.00057
NM_005529.7(HSPG2):c.6541G>A (p.Ala2181Thr)	rs143109401	0.00056
NM_005529.7(HSPG2):c.2549G>A (p.Arg850His)	rs140392638	0.00054
NM_005529.7(HSPG2):c.1557G>A (p.Leu519=)	rs149710901	0.00051
NM_005529.7(HSPG2):c.5705G>A (p.Gly1902Asp)	rs553885469	0.00051
NM_005529.7(HSPG2):c.8605G>C (p.Ala2869Pro)	rs139838884	0.00046
NM_005529.7(HSPG2):c.4396-5C>T	rs117917442	0.00040
NM_005529.7(HSPG2):c.7826G>A (p.Arg2609Gln)	rs147286334	0.00039
NM_005529.7(HSPG2):c.87C>T (p.Tyr29=)	rs368430410	0.00031
NM_005529.7(HSPG2):c.8961C>T (p.Gly2987=)	rs369899077	0.00028
NM_005529.7(HSPG2):c.11496C>T (p.Phe3832=)	rs536882233	0.00027
NM_005529.7(HSPG2):c.9030G>A (p.Pro3010=)	rs202067055	0.00026
NM_005529.7(HSPG2):c.5297C>T (p.Ala1766Val)	rs139794766	0.00025
NM_005529.7(HSPG2):c.6105G>A (p.Gln2035=)	rs371397998	0.00025
NM_005529.7(HSPG2):c.9411C>T (p.Ala3137=)	rs533824462	0.00025
NM_005529.7(HSPG2):c.9060G>A (p.Arg3020=)	rs372508479	0.00024
NM_005529.7(HSPG2):c.4971C>T (p.Tyr1657=)	rs138459752	0.00023
NM_005529.7(HSPG2):c.5646G>A (p.Leu1882=)	rs533624001	0.00017
NM_005529.7(HSPG2):c.12354G>A (p.Thr4118=)	rs371885206	0.00016
NM_005529.7(HSPG2):c.1549G>A (p.Ala517Thr)	rs139719757	0.00016
NM_005529.7(HSPG2):c.1372G>A (p.Glu458Lys)	rs531029732	0.00013
NM_005529.7(HSPG2):c.1844G>A (p.Arg615His)	rs189089389	0.00010
NM_005529.7(HSPG2):c.4758C>T (p.Ala1586=)	rs374708543	0.00010
NM_005529.7(HSPG2):c.5934G>A (p.Arg1978=)	rs557762861	0.00007
NM_005529.7(HSPG2):c.4928C>A (p.Pro1643His)	rs775389963	0.00006
NM_005529.7(HSPG2):c.9033_9034del (p.Pro3011_Ser3012insTer)	rs1318029350	0.00003
NM_005529.7(HSPG2):c.253C>T (p.Arg85Ter)	rs747493127	0.00001
NM_005529.7(HSPG2):c.4275A>G (p.Pro1425=)	rs540961117	0.00001
NM_005529.7(HSPG2):c.11671+10C>T	rs540252244
NM_005529.7(HSPG2):c.11717G>A (p.Arg3906Gln)	rs78944354
NM_005529.7(HSPG2):c.12110G>T (p.Arg4037Leu)	rs143015575
NM_005529.7(HSPG2):c.3707C>A (p.Ala1236Glu)	rs113652076
NM_005529.7(HSPG2):c.8545G>T (p.Val2849Leu)	rs147114700

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. The submitted information has not been verified. If you have questions about the information contained on this website, please see a health care professional.