Variants with conflicting interpretations studied for LAMA2-related muscular dystrophy

Minimum review status of the submission for LAMA2-related muscular dystrophy:		Collection method of the submission for LAMA2-related muscular dystrophy:
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
4204	109	0	60	47	0	2	109

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
LAMA2-related muscular dystrophy		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	0	55	0	0	0
	likely pathogenic	24	0	2	0	0
	uncertain significance	0	2	0	2	1
	likely benign	0	0	38	0	0
	benign	0	0	9	5	0

Condition to condition summary #

Total conditions: 2

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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
Merosin deficient congenital muscular dystrophy; Muscular dystrophy, limb-girdle, autosomal recessive 23	0	82	0	40	44	0	2	86
LAMA2-related muscular dystrophy	4351	42	0	24	3	0	2	29

All variants with conflicting interpretations #

Total variants: 109

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HGVS	dbSNP	gnomAD frequency
NM_000426.4(LAMA2):c.8528A>G (p.Asn2843Ser)	rs73599293	0.02027
NM_000426.4(LAMA2):c.3613A>G (p.Thr1205Ala)	rs35889149	0.01170
NM_000426.4(LAMA2):c.8548-10T>C	rs113644365	0.00865
NM_000426.4(LAMA2):c.8774C>T (p.Pro2925Leu)	rs77113162	0.00635
NM_000426.4(LAMA2):c.6150T>C (p.Asp2050=)	rs114766691	0.00339
NM_000426.4(LAMA2):c.2462C>T (p.Thr821Met)	rs117422805	0.00169
NM_000426.4(LAMA2):c.9211+6T>C	rs201375881	0.00085
NM_000426.4(LAMA2):c.946G>A (p.Asp316Asn)	rs141340479	0.00067
NM_000426.4(LAMA2):c.3532G>A (p.Ala1178Thr)	rs34505698	0.00066
NM_000426.4(LAMA2):c.7250A>G (p.His2417Arg)	rs147185142	0.00052
NM_000426.4(LAMA2):c.3244C>T (p.His1082Tyr)	rs146490004	0.00028
NM_000426.4(LAMA2):c.6832A>G (p.Met2278Val)	rs146854942	0.00025
NM_000426.4(LAMA2):c.4010A>G (p.His1337Arg)	rs139739075	0.00024
NM_000426.4(LAMA2):c.4205G>A (p.Arg1402His)	rs144830879	0.00024
NM_000426.4(LAMA2):c.5405G>T (p.Arg1802Leu)	rs141235562	0.00022
NM_000426.4(LAMA2):c.8905C>T (p.Arg2969Cys)	rs374888837	0.00020
NM_000426.4(LAMA2):c.7088C>T (p.Thr2363Ile)	rs371403343	0.00017
NM_000426.4(LAMA2):c.7057C>T (p.Arg2353Cys)	rs145885540	0.00016
NM_000426.4(LAMA2):c.4969G>A (p.Val1657Met)	rs370971334	0.00014
NM_000426.4(LAMA2):c.542A>G (p.Asn181Ser)	rs143664472	0.00014
NM_000426.4(LAMA2):c.8011C>A (p.Pro2671Thr)	rs780695627	0.00014
NM_000426.4(LAMA2):c.4993G>A (p.Gly1665Arg)	rs373997222	0.00012
NM_000426.4(LAMA2):c.6322C>T (p.Arg2108Trp)	rs139824017	0.00012
NM_000426.4(LAMA2):c.1084A>T (p.Arg362Ter)	rs191912891	0.00011
NM_000426.4(LAMA2):c.1373G>A (p.Arg458Lys)	rs140604077	0.00011
NM_000426.4(LAMA2):c.8842G>A (p.Gly2948Ser)	rs143638361	0.00011
NM_000426.4(LAMA2):c.1816A>G (p.Ile606Val)	rs113022759	0.00010
NM_000426.4(LAMA2):c.2240G>C (p.Gly747Ala)	rs139843107	0.00010
NM_000426.4(LAMA2):c.9161C>A (p.Ala3054Glu)	rs151049890	0.00010
NM_000426.4(LAMA2):c.1391C>T (p.Pro464Leu)	rs150394215	0.00009
NM_000426.4(LAMA2):c.553C>T (p.Arg185Cys)	rs777977352	0.00009
NM_000426.4(LAMA2):c.3862G>A (p.Val1288Ile)	rs758134778	0.00008
NM_000426.4(LAMA2):c.4075A>G (p.Met1359Val)	rs749372185	0.00008
NM_000426.4(LAMA2):c.6563G>A (p.Ser2188Asn)	rs372592018	0.00008
NM_000426.4(LAMA2):c.8388A>C (p.Glu2796Asp)	rs184127828	0.00007
NM_000426.4(LAMA2):c.8524A>G (p.Ile2842Val)	rs140178576	0.00007
NM_000426.4(LAMA2):c.409G>A (p.Ala137Thr)	rs368349321	0.00006
NM_000426.4(LAMA2):c.437C>G (p.Ser146Cys)	rs143680577	0.00006
NM_000426.4(LAMA2):c.7486C>T (p.Leu2496Phe)	rs970365005	0.00006
NM_000426.4(LAMA2):c.8836G>A (p.Gly2946Arg)	rs370843758	0.00006
NM_000426.4(LAMA2):c.7681G>A (p.Gly2561Ser)	rs200341138	0.00005
NM_000426.4(LAMA2):c.7978C>A (p.Leu2660Ile)	rs201587923	0.00005
NM_000426.4(LAMA2):c.8570A>G (p.Gln2857Arg)	rs372956200	0.00005
NM_000426.4(LAMA2):c.830C>T (p.Ser277Leu)	rs398123388	0.00004
NM_000426.4(LAMA2):c.8497G>T (p.Asp2833Tyr)	rs794727815	0.00004
NM_000426.4(LAMA2):c.2477G>A (p.Arg826Gln)	rs759973830	0.00003
NM_000426.4(LAMA2):c.4471G>A (p.Asp1491Asn)	rs375640462	0.00003
NM_000426.4(LAMA2):c.4960-17C>A	rs758048596	0.00003
NM_000426.4(LAMA2):c.5477G>A (p.Arg1826Gln)	rs373614496	0.00003
NM_000426.4(LAMA2):c.9014C>T (p.Ala3005Val)	rs75048006	0.00003
NM_000426.4(LAMA2):c.1495C>T (p.Arg499Cys)	rs143626559	0.00002
NM_000426.4(LAMA2):c.283+1G>A	rs200288072	0.00002
NM_000426.4(LAMA2):c.4188G>A (p.Pro1396=)	rs369076029	0.00002
NM_000426.4(LAMA2):c.4876C>T (p.Gln1626Ter)	rs369776766	0.00002
NM_000426.4(LAMA2):c.6429+1G>T	rs1262029350	0.00002
NM_000426.4(LAMA2):c.7377dup (p.Leu2460fs)	rs749566145	0.00002
NM_000426.4(LAMA2):c.8890G>T (p.Val2964Leu)	rs202159946	0.00002
NM_000426.4(LAMA2):c.112+1G>A	rs398123367	0.00001
NM_000426.4(LAMA2):c.1303C>T (p.Arg435Ter)	rs773209126	0.00001
NM_000426.4(LAMA2):c.2584T>C (p.Cys862Arg)	rs121913573	0.00001
NM_000426.4(LAMA2):c.2749+1G>C	rs759555791	0.00001
NM_000426.4(LAMA2):c.2749+2dup	rs759144210	0.00001
NM_000426.4(LAMA2):c.2T>C (p.Met1Thr)	rs374403765	0.00001
NM_000426.4(LAMA2):c.3038-7G>A	rs767841898	0.00001
NM_000426.4(LAMA2):c.3556-13T>A	rs775278003	0.00001
NM_000426.4(LAMA2):c.3829C>T (p.Arg1277Ter)	rs1554269891	0.00001
NM_000426.4(LAMA2):c.442C>T (p.Arg148Trp)	rs752485547	0.00001
NM_000426.4(LAMA2):c.4640C>T (p.Thr1547Met)	rs778106503	0.00001
NM_000426.4(LAMA2):c.4717+1G>T	rs1131691660	0.00001
NM_000426.4(LAMA2):c.4858A>T (p.Lys1620Ter)	rs762342110	0.00001
NM_000426.4(LAMA2):c.5602G>T (p.Glu1868Ter)	rs1276300668	0.00001
NM_000426.4(LAMA2):c.5706_5712del (p.Asp1902fs)	rs398123377	0.00001
NM_000426.4(LAMA2):c.6993-2A>C	rs200669208	0.00001
NM_000426.4(LAMA2):c.7898+12A>G	rs572960610	0.00001
NM_000426.4(LAMA2):c.8244+1G>A	rs749522728	0.00001
NM_000426.4(LAMA2):c.8703+1G>A	rs1446002589	0.00001
NM_000426.4(LAMA2):c.8770C>T (p.Gln2924Ter)	rs1034133545	0.00001
NM_000426.4(LAMA2):c.1233C>A (p.Cys411Ter)	rs1583169005
NM_000426.4(LAMA2):c.1467+2T>C	rs1554234163
NM_000426.4(LAMA2):c.184G>T (p.Gly62Ter)	rs398123368
NM_000426.4(LAMA2):c.2658T>A (p.Cys886Ter)	rs1789395190
NM_000426.4(LAMA2):c.2749+1G>A	rs759555791
NM_000426.4(LAMA2):c.2916del (p.Phe972fs)	rs2482334983
NM_000426.4(LAMA2):c.3235T>C (p.Cys1079Arg)	rs1583469739
NM_000426.4(LAMA2):c.3623_3645del (p.Lys1208fs)	rs727503992
NM_000426.4(LAMA2):c.437C>A (p.Ser146Tyr)	rs143680577
NM_000426.4(LAMA2):c.437C>T (p.Ser146Phe)	rs143680577
NM_000426.4(LAMA2):c.4523G>A (p.Arg1508Lys)	rs770084568
NM_000426.4(LAMA2):c.5038G>T (p.Glu1680Ter)	rs1778794887
NM_000426.4(LAMA2):c.504T>A (p.Tyr168Ter)	rs1008335405
NM_000426.4(LAMA2):c.5374G>T (p.Glu1792Ter)	rs746201268
NM_000426.4(LAMA2):c.5910T>A (p.Cys1970Ter)	rs1781395670
NM_000426.4(LAMA2):c.6305T>G (p.Leu2102Ter)	rs1782333085
NM_000426.4(LAMA2):c.6444_6445del (p.Ser2149fs)	rs2533416225
NM_000426.4(LAMA2):c.6510TGT[1] (p.Val2172del)	rs1363017615
NM_000426.4(LAMA2):c.6617del (p.Phe2206fs)	rs867012156
NM_000426.4(LAMA2):c.6820del (p.Asp2274fs)	rs1562581261
NM_000426.4(LAMA2):c.6894dup (p.Phe2299fs)
NM_000426.4(LAMA2):c.7042dup (p.Tyr2348fs)	rs2533441401
NM_000426.4(LAMA2):c.7810C>T (p.Arg2604Ter)	rs766920075
NM_000426.4(LAMA2):c.7881T>G (p.His2627Gln)	rs202247792
NM_000426.4(LAMA2):c.8188C>T (p.Gln2730Ter)	rs1784919273
NM_000426.4(LAMA2):c.8244+3_8244+6del	rs746678525
NM_000426.4(LAMA2):c.828C>G (p.Tyr276Ter)	rs1028599119
NM_000426.4(LAMA2):c.8692del (p.Arg2898fs)	rs1785973861
NM_000426.4(LAMA2):c.9149_9155del (p.Ser3050fs)	rs1323340608
NM_000426.4(LAMA2):c.9222del (p.Lys3074fs)	rs1787058325
NM_000426.4(LAMA2):c.9253C>T (p.Arg3085Ter)	rs121913571
NM_000426.4(LAMA2):c.951_952insCT (p.Cys318fs)	rs1554227092

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