ClinVar Miner

Variants with conflicting interpretations studied for Bethlem myopathy 1

Coded as:
Minimum review status of the submission for Bethlem myopathy 1: Collection method of the submission for Bethlem myopathy 1:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:
ClinVar version:

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
5453 69 0 13 27 0 13 53

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
Bethlem myopathy 1 pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 10 2 0 0
likely pathogenic 10 0 5 3 3
uncertain significance 2 5 0 22 5
likely benign 0 3 22 0 3
benign 0 3 5 3 0

Condition to condition summary #

Total conditions: 1
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
Bethlem myopathy 1 5453 69 0 13 27 0 13 53

All variants with conflicting interpretations #

Total variants: 53
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001849.4(COL6A2):c.1466G>A (p.Arg489Gln) rs61735828 0.00627
NM_001849.4(COL6A2):c.2795C>T (p.Pro932Leu) rs117725825 0.00233
NM_001849.4(COL6A2):c.2558G>A (p.Arg853Gln) rs144830948 0.00148
NM_004369.4(COL6A3):c.7258C>T (p.Arg2420Trp) rs150165484 0.00131
NM_001849.4(COL6A2):c.511G>A (p.Gly171Arg) rs200710788 0.00116
NM_004369.4(COL6A3):c.7447A>G (p.Lys2483Glu) rs139260335 0.00057
NM_001848.3(COL6A1):c.2876T>C (p.Val959Ala) rs144814689 0.00050
NM_001848.3(COL6A1):c.2857G>A (p.Ala953Thr) rs150378645 0.00038
NM_004369.4(COL6A3):c.4912G>A (p.Ala1638Thr) rs114322958 0.00031
NM_001849.4(COL6A2):c.*5G>A rs377195134 0.00026
NM_004369.4(COL6A3):c.3556G>A (p.Val1186Met) rs144976132 0.00019
NM_004369.4(COL6A3):c.2305G>A (p.Ala769Thr) rs142719863 0.00010
NM_004369.4(COL6A3):c.6422C>A (p.Pro2141His) rs369169235 0.00010
NM_004369.4(COL6A3):c.1292C>T (p.Pro431Leu) rs144746928 0.00008
NM_001848.3(COL6A1):c.1684A>G (p.Ile562Val) rs374315921 0.00007
NM_001848.3(COL6A1):c.2911G>A (p.Val971Met) rs769795690 0.00006
NM_001848.3(COL6A1):c.717+4A>G rs762867111 0.00006
NM_004369.4(COL6A3):c.6898G>A (p.Gly2300Arg) rs763348222 0.00006
NM_001848.3(COL6A1):c.1694G>A (p.Arg565Gln) rs886057155 0.00005
NM_001848.3(COL6A1):c.994G>A (p.Gly332Ser) rs11701912 0.00005
NM_001848.3(COL6A1):c.1945G>A (p.Glu649Lys) rs764129993 0.00004
NM_001849.4(COL6A2):c.2153G>A (p.Ser718Asn) rs368641951 0.00004
NM_004369.4(COL6A3):c.2303G>A (p.Arg768His) rs575412915 0.00004
NM_004369.4(COL6A3):c.4121A>T (p.Asp1374Val) rs766488017 0.00004
NM_001848.3(COL6A1):c.1960G>A (p.Glu654Lys) rs375318905 0.00003
NM_004369.4(COL6A3):c.7660G>A (p.Ala2554Thr) rs786205870 0.00003
NM_001848.3(COL6A1):c.821C>T (p.Pro274Leu) rs201093313 0.00002
NM_004369.4(COL6A3):c.3700G>A (p.Val1234Met) rs747082651 0.00002
NM_001849.4(COL6A2):c.2099G>A (p.Gly700Asp) rs2078657536 0.00001
NM_001849.4(COL6A2):c.2483C>T (p.Thr828Met) rs755782924 0.00001
NM_001849.4(COL6A2):c.2611G>A (p.Asp871Asn) rs387906610 0.00001
NM_001849.4(COL6A2):c.287A>G (p.Tyr96Cys) rs2078408746 0.00001
NM_004369.4(COL6A3):c.1022G>A (p.Arg341His) rs140510298 0.00001
NM_004369.4(COL6A3):c.2665C>T (p.Arg889Cys) rs201327438 0.00001
NM_004369.4(COL6A3):c.3220G>A (p.Asp1074Asn) rs778403814 0.00001
NM_004369.4(COL6A3):c.575C>T (p.Pro192Leu) rs563800854 0.00001
NM_004369.4(COL6A3):c.5950C>T (p.Arg1984Ter) rs771941724 0.00001
NM_001848.3(COL6A1):c.1056+1G>A rs398123631
NM_001848.3(COL6A1):c.1056+1del rs1556425853
NM_001848.3(COL6A1):c.1056+2T>A
NM_001848.3(COL6A1):c.1123G>A (p.Glu375Lys)
NM_001848.3(COL6A1):c.1226C>A (p.Ala409Glu) rs765826390
NM_001848.3(COL6A1):c.631C>T (p.Arg211Cys) rs375217284
NM_001848.3(COL6A1):c.782_789del (p.Leu261fs) rs886043354
NM_001849.4(COL6A2):c.2093C>T (p.Ala698Val) rs1085307668
NM_001849.4(COL6A2):c.2096G>A (p.Gly699Asp) rs863224861
NM_001849.4(COL6A2):c.2192C>T (p.Thr731Met) rs794727419
NM_001849.4(COL6A2):c.2329T>C (p.Cys777Arg) rs267606747
NM_001849.4(COL6A2):c.403G>A (p.Asp135Asn) rs983938730
NM_004369.4(COL6A3):c.1630C>T (p.Arg544Trp)
NM_004369.4(COL6A3):c.3844G>A (p.Val1282Met) rs535661345
NM_004369.4(COL6A3):c.6309G>C (p.Lys2103Asn) rs1574975196
NM_004369.4(COL6A3):c.7264C>T (p.Arg2422Ter) rs878854379

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