Variants with conflicting interpretations studied for Autosomal recessive nonsyndromic hearing loss 77

Minimum review status of the submission for Autosomal recessive nonsyndromic hearing loss 77:		Collection method of the submission for Autosomal recessive nonsyndromic hearing loss 77:
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
655	98	0	35	53	0	11	90

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
Autosomal recessive nonsyndromic hearing loss 77		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	0	18	0	0	0
	likely pathogenic	18	0	11	0	0
	uncertain significance	0	11	0	39	23
	likely benign	0	0	39	0	17
	benign	0	0	23	17	0

Condition to condition summary #

Total conditions: 1

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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
Autosomal recessive nonsyndromic hearing loss 77	655	98	0	35	53	0	11	90

All variants with conflicting interpretations #

Total variants: 90

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HGVS	dbSNP	gnomAD frequency
NM_001384474.1(LOXHD1):c.2175C>T (p.Asn725=)	rs2086005	0.09034
NM_001384474.1(LOXHD1):c.5399+13G>A	rs59128481	0.07033
NM_001384474.1(LOXHD1):c.4868A>G (p.Glu1623Gly)	rs12606417	0.06969
NM_001384474.1(LOXHD1):c.1087G>A (p.Val363Ile)	rs10163657	0.05881
NM_001384474.1(LOXHD1):c.2T>A (p.Met1Lys)	rs36024592	0.02382
NM_001384474.1(LOXHD1):c.966G>C (p.Gly322=)	rs114082868	0.01931
NM_001384474.1(LOXHD1):c.2370C>T (p.Asp790=)	rs34723936	0.01692
NM_001384474.1(LOXHD1):c.1876G>T (p.Gly626Cys)	rs34589386	0.01503
NM_001384474.1(LOXHD1):c.3269G>A (p.Arg1090Gln)	rs118174674	0.01368
NM_001384474.1(LOXHD1):c.2080G>T (p.Asp694Tyr)	rs35727744	0.01099
NM_001384474.1(LOXHD1):c.1742T>C (p.Val581Ala)	rs35007621	0.00961
NM_001384474.1(LOXHD1):c.4526G>A (p.Gly1509Glu)	rs187587197	0.00751
NM_001384474.1(LOXHD1):c.1028G>A (p.Arg343His)	rs183531840	0.00717
NM_001384474.1(LOXHD1):c.2027A>G (p.Asp676Gly)	rs16978578	0.00715
NM_001384474.1(LOXHD1):c.611-15T>C	rs146912450	0.00662
NM_001384474.1(LOXHD1):c.274G>A (p.Val92Ile)	rs115275492	0.00656
NM_001384474.1(LOXHD1):c.1431+10G>T	rs57330753	0.00648
NM_001384474.1(LOXHD1):c.3999C>T (p.Cys1333=)	rs117297079	0.00630
NM_001384474.1(LOXHD1):c.1843C>A (p.Arg615=)	rs112463030	0.00507
NM_001384474.1(LOXHD1):c.2871G>A (p.Ser957=)	rs181591912	0.00456
NM_001384474.1(LOXHD1):c.457C>T (p.Arg153Cys)	rs112618498	0.00404
NM_001384474.1(LOXHD1):c.6034G>A (p.Glu2012Lys)	rs79045813	0.00339
NM_001384474.1(LOXHD1):c.1945G>A (p.Asp649Asn)	rs141932807	0.00334
NM_001384474.1(LOXHD1):c.1708G>A (p.Asp570Asn)	rs140437150	0.00330
NM_001384474.1(LOXHD1):c.5802C>A (p.Asn1934Lys)	rs61733519	0.00307
NM_001384474.1(LOXHD1):c.6270G>A (p.Arg2090=)	rs367833904	0.00296
NM_001384474.1(LOXHD1):c.1570C>T (p.Arg524Cys)	rs192376005	0.00283
NM_001384474.1(LOXHD1):c.5689C>T (p.Leu1897=)	rs202043044	0.00218
NM_001384474.1(LOXHD1):c.4822G>A (p.Val1608Ile)	rs140042576	0.00203
NM_001384474.1(LOXHD1):c.3090G>A (p.Thr1030=)	rs113994614	0.00173
NM_001384474.1(LOXHD1):c.5313C>T (p.Gly1771=)	rs373924055	0.00168
NM_001384474.1(LOXHD1):c.1617G>A (p.Met539Ile)	rs143142227	0.00160
NM_001384474.1(LOXHD1):c.5023C>T (p.Arg1675Cys)	rs201060702	0.00149
NM_001384474.1(LOXHD1):c.6099C>T (p.Asn2033=)	rs146200756	0.00145
NM_001384474.1(LOXHD1):c.3024C>T (p.Val1008=)	rs370616818	0.00138
NM_001384474.1(LOXHD1):c.2914G>A (p.Glu972Lys)	rs367630521	0.00123
NM_001384474.1(LOXHD1):c.4217C>T (p.Ala1406Val)	rs146739496	0.00111
NM_001384474.1(LOXHD1):c.4440G>A (p.Val1480=)	rs76946640	0.00098
NM_001384474.1(LOXHD1):c.6599G>A (p.Arg2200Gln)	rs148468627	0.00074
NM_001384474.1(LOXHD1):c.1815C>T (p.Asp605=)	rs201388780	0.00071
NM_001384474.1(LOXHD1):c.5853G>A (p.Lys1951=)	rs201366522	0.00069
NM_001384474.1(LOXHD1):c.4480C>T (p.Arg1494Ter)	rs201587138	0.00063
NM_001384474.1(LOXHD1):c.1716C>T (p.Asn572=)	rs147582935	0.00047
NM_001384474.1(LOXHD1):c.1944C>T (p.Ser648=)	rs369039902	0.00034
NM_001384474.1(LOXHD1):c.1313A>G (p.Lys438Arg)	rs186138859	0.00033
NM_001384474.1(LOXHD1):c.5400-3C>T	rs528236655	0.00029
NM_001384474.1(LOXHD1):c.4824C>G (p.Val1608=)	rs114557260	0.00028
NM_001384474.1(LOXHD1):c.4031G>T (p.Cys1344Phe)	rs368870055	0.00027
NM_001384474.1(LOXHD1):c.231C>T (p.Leu77=)	rs200306249	0.00026
NM_001384474.1(LOXHD1):c.6243T>C (p.Cys2081=)	rs199645176	0.00026
NM_001384474.1(LOXHD1):c.1571G>A (p.Arg524His)	rs187658135	0.00022
NM_001384474.1(LOXHD1):c.1887C>T (p.Ser629=)	rs189550119	0.00022
NM_001384474.1(LOXHD1):c.1970+9G>A	rs532438706	0.00022
NM_001384474.1(LOXHD1):c.1730T>G (p.Leu577Arg)	rs727503147	0.00017
NM_001384474.1(LOXHD1):c.3951C>A (p.Val1317=)	rs779507390	0.00015
NM_001384474.1(LOXHD1):c.2863G>C (p.Glu955Gln)	rs548893604	0.00013
NM_001384474.1(LOXHD1):c.5584C>T (p.Arg1862Trp)	rs201994383	0.00013
NM_001384474.1(LOXHD1):c.1759C>T (p.Arg587Trp)	rs540100675	0.00011
NM_001384474.1(LOXHD1):c.4068G>A (p.Arg1356=)	rs539688337	0.00009
NM_001384474.1(LOXHD1):c.6071C>T (p.Thr2024Met)	rs369043488	0.00007
NM_001384474.1(LOXHD1):c.3061+1G>A	rs537227442	0.00006
NM_001384474.1(LOXHD1):c.3936C>G (p.Leu1312=)	rs533251927	0.00006
NM_001384474.1(LOXHD1):c.6252C>T (p.His2084=)	rs753440039	0.00006
NM_001384474.1(LOXHD1):c.6539G>A (p.Gly2180Glu)	rs763915229	0.00006
NM_001384474.1(LOXHD1):c.5224C>T (p.Arg1742Cys)	rs561122654	0.00004
NM_001384474.1(LOXHD1):c.2245-13G>A	rs749554659	0.00003
NM_001384474.1(LOXHD1):c.2497C>T (p.Arg833Ter)	rs188119157	0.00003
NM_001384474.1(LOXHD1):c.442A>T (p.Lys148Ter)	rs886044666	0.00003
NM_001384474.1(LOXHD1):c.71del (p.Leu24fs)	rs775267638	0.00003
NM_001384474.1(LOXHD1):c.4212+1G>A	rs889110926	0.00002
NM_001384474.1(LOXHD1):c.6333C>T (p.Tyr2111=)	rs374858340	0.00002
NM_001384474.1(LOXHD1):c.4282C>T (p.Arg1428Ter)	rs932266011	0.00001
NM_001384474.1(LOXHD1):c.4794_4795insTC (p.Ile1599fs)	rs1598914701	0.00001
NM_001384474.1(LOXHD1):c.4936C>T (p.Arg1646Ter)	rs960741408	0.00001
NM_001384474.1(LOXHD1):c.4940C>A (p.Ala1647Asp)	rs1459136471	0.00001
NM_001384474.1(LOXHD1):c.5731G>A (p.Gly1911Arg)	rs780560784	0.00001
NM_001384474.1(LOXHD1):c.6130C>T (p.Arg2044Ter)	rs1306586204	0.00001
NM_001384474.1(LOXHD1):c.1537_1538del (p.Leu513fs)	rs1555683951
NM_001384474.1(LOXHD1):c.1894G>T (p.Gly632Cys)	rs35088381
NM_001384474.1(LOXHD1):c.2696G>C (p.Arg899Pro)	rs745683775
NM_001384474.1(LOXHD1):c.2816AGA[3] (p.Lys942del)	rs142960762
NM_001384474.1(LOXHD1):c.2874_2891dup (p.Ser960_Ser965dup)	rs759237437
NM_001384474.1(LOXHD1):c.3281A>G (p.Asp1094Gly)	rs543098936
NM_001384474.1(LOXHD1):c.3351-1G>A	rs868646051
NM_001384474.1(LOXHD1):c.3924C>A (p.Tyr1308Ter)	rs184966970
NM_001384474.1(LOXHD1):c.4148C>T (p.Thr1383Met)	rs7244681
NM_001384474.1(LOXHD1):c.4595_4605del (p.Asp1532fs)
NM_001384474.1(LOXHD1):c.4714C>T (p.Arg1572Ter)	rs75949023
NM_001384474.1(LOXHD1):c.5330del (p.Asn1777fs)	rs776345911
NM_001384474.1(LOXHD1):c.6050-2A>C

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