Variants with conflicting interpretations studied for ATM-related disorder

Minimum review status of the submission for ATM-related disorder:		Collection method of the submission for ATM-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
80	189	1	58	80	0	4	126

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
ATM-related disorder		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	1	6	0	0	0
	likely pathogenic	2	0	1	0	0
	uncertain significance	0	2	0	43	6
	likely benign	0	1	37	0	47
	benign	0	0	0	3	0

Condition to condition summary #

Total conditions: 6

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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 clinically significant conflict (e.g. benign vs pathogenic)	Variants with any conflict
not provided	194	0	32	61	4	89
not specified	151	0	33	42	0	69
Breast and/or ovarian cancer	59	0	3	7	0	10
Hereditary cancer	6	0	0	8	0	8
Tip-toe gait	1	0	2	0	0	2
Breast cancer, susceptibility to	0	1	0	0	0	1

All variants with conflicting interpretations #

Total variants: 126

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HGVS	dbSNP	gnomAD frequency
NM_000051.4(ATM):c.5793T>C (p.Ala1931=)	rs3092910	0.00608
NM_000051.4(ATM):c.1810C>T (p.Pro604Ser)	rs2227922	0.00431
NM_000051.4(ATM):c.1229T>C (p.Val410Ala)	rs56128736	0.00185
NM_000051.4(ATM):c.2608A>G (p.Asn870Asp)	rs61734354	0.00130
NM_000051.4(ATM):c.6176C>T (p.Thr2059Ile)	rs144761622	0.00117
NM_000051.4(ATM):c.6860G>C (p.Gly2287Ala)	rs1800061	0.00096
NM_000051.4(ATM):c.1073A>G (p.Asn358Ser)	rs149636614	0.00079
NM_000051.4(ATM):c.2096A>G (p.Glu699Gly)	rs147934285	0.00078
NM_000051.4(ATM):c.6988C>G (p.Leu2330Val)	rs148432863	0.00075
NM_000051.4(ATM):c.334G>A (p.Ala112Thr)	rs146382972	0.00072
NM_000051.4(ATM):c.320G>A (p.Cys107Tyr)	rs142358238	0.00062
NM_000051.4(ATM):c.6543G>T (p.Glu2181Asp)	rs138828590	0.00054
NM_000051.4(ATM):c.4424A>G (p.Tyr1475Cys)	rs34640941	0.00053
NM_000051.4(ATM):c.8592C>T (p.Tyr2864=)	rs56025670	0.00051
NM_000051.4(ATM):c.7313C>T (p.Thr2438Ile)	rs147604227	0.00050
NM_000051.4(ATM):c.4709T>C (p.Val1570Ala)	rs140856217	0.00043
NM_000051.4(ATM):c.7390T>C (p.Cys2464Arg)	rs55801750	0.00038
NM_000051.4(ATM):c.7740A>C (p.Arg2580Ser)	rs199915459	0.00031
NM_000051.4(ATM):c.2494C>T (p.Arg832Cys)	rs2229022	0.00029
NM_000051.4(ATM):c.4082A>G (p.Gln1361Arg)	rs141921797	0.00029
NM_000051.4(ATM):c.4324T>C (p.Tyr1442His)	rs201666889	0.00029
NM_000051.4(ATM):c.3014A>G (p.Asn1005Ser)	rs146531614	0.00028
NM_000051.4(ATM):c.7004C>T (p.Thr2335Ile)	rs3092831	0.00028
NM_000051.4(ATM):c.1595G>A (p.Cys532Tyr)	rs35963548	0.00026
NM_000051.4(ATM):c.4362A>C (p.Lys1454Asn)	rs148993589	0.00025
NM_000051.4(ATM):c.5975A>C (p.Lys1992Thr)	rs150757822	0.00025
NM_000051.4(ATM):c.2281A>T (p.Thr761Ser)	rs2235011	0.00021
NM_000051.4(ATM):c.4871A>G (p.His1624Arg)	rs56354559	0.00021
NM_000051.4(ATM):c.295A>G (p.Ser99Gly)	rs137882485	0.00019
NM_000051.4(ATM):c.5489T>C (p.Met1830Thr)	rs145812395	0.00019
NM_000051.4(ATM):c.5821G>C (p.Val1941Leu)	rs147187700	0.00019
NM_000051.4(ATM):c.7475T>G (p.Leu2492Arg)	rs56399857	0.00019
NM_000051.4(ATM):c.4060C>A (p.Pro1354Thr)	rs145119475	0.00017
NM_000051.4(ATM):c.3403-16_3403-15insA	rs569564716	0.00016
NM_000051.4(ATM):c.7224G>A (p.Ser2408=)	rs145747513	0.00016
NM_000051.4(ATM):c.7381C>T (p.Arg2461Cys)	rs201314561	0.00016
NM_000051.4(ATM):c.3077+4G>A	rs201222237	0.00015
NM_000051.4(ATM):c.8584+10T>C	rs373321041	0.00015
NM_000051.4(ATM):c.9086G>A (p.Gly3029Asp)	rs201199629	0.00015
NM_000051.4(ATM):c.4066A>G (p.Asn1356Asp)	rs147600485	0.00014
NM_000051.4(ATM):c.8560C>T (p.Arg2854Cys)	rs201958469	0.00013
NM_000051.4(ATM):c.2346A>G (p.Leu782=)	rs730881285	0.00011
NM_000051.4(ATM):c.2466+7A>G	rs55812024	0.00010
NM_000051.4(ATM):c.5890A>G (p.Lys1964Glu)	rs201963507	0.00010
NM_000051.4(ATM):c.7494T>C (p.Ser2498=)	rs34393781	0.00010
NM_000051.4(ATM):c.1351C>T (p.Arg451Cys)	rs201719927	0.00009
NM_000051.4(ATM):c.1911A>G (p.Gln637=)	rs764790965	0.00009
NM_000051.4(ATM):c.332-3T>C	rs376116157	0.00009
NM_000051.4(ATM):c.4414T>G (p.Leu1472Val)	rs539676759	0.00009
NM_000051.4(ATM):c.5005+7_5005+8del	rs587780626	0.00009
NM_000051.4(ATM):c.5583G>A (p.Leu1861=)	rs781383087	0.00009
NM_000051.4(ATM):c.6382T>C (p.Leu2128=)	rs753646931	0.00009
NM_000051.4(ATM):c.670A>G (p.Lys224Glu)	rs145053092	0.00009
NM_000051.4(ATM):c.2021A>G (p.His674Arg)	rs201762714	0.00007
NM_000051.4(ATM):c.496+4T>C	rs587781375	0.00007
NM_000051.4(ATM):c.115A>G (p.Thr39Ala)	rs779297339	0.00006
NM_000051.4(ATM):c.198A>G (p.Lys66=)	rs540920248	0.00006
NM_000051.4(ATM):c.2804C>T (p.Thr935Met)	rs3218708	0.00006
NM_000051.4(ATM):c.3588A>G (p.Lys1196=)	rs376524625	0.00006
NM_000051.4(ATM):c.5352C>T (p.Asn1784=)	rs140641762	0.00006
NM_000051.4(ATM):c.610G>A (p.Gly204Arg)	rs147915571	0.00006
NM_000051.4(ATM):c.6315G>C (p.Arg2105Ser)	rs587780632	0.00006
NM_000051.4(ATM):c.7062G>A (p.Ala2354=)	rs143489373	0.00006
NM_000051.4(ATM):c.7271T>G (p.Val2424Gly)	rs28904921	0.00006
NM_000051.4(ATM):c.2919A>G (p.Leu973=)	rs587779829	0.00005
NM_000051.4(ATM):c.7983T>C (p.Asp2661=)	rs143972422	0.00005
NM_000051.4(ATM):c.8147T>C (p.Val2716Ala)	rs587782652	0.00005
NM_000051.4(ATM):c.861T>C (p.Ile287=)	rs55849405	0.00005
NM_000051.4(ATM):c.1516G>T (p.Gly506Cys)	rs587779816	0.00004
NM_000051.4(ATM):c.1888G>A (p.Val630Met)	rs148191382	0.00004
NM_000051.4(ATM):c.2610C>T (p.Asn870=)	rs587780618	0.00004
NM_000051.4(ATM):c.3468G>A (p.Thr1156=)	rs148358896	0.00004
NM_000051.4(ATM):c.4606A>G (p.Lys1536Glu)	rs587779841	0.00004
NM_000051.4(ATM):c.5763-1050A>G	rs774925473	0.00004
NM_000051.4(ATM):c.7592T>C (p.Met2531Thr)	rs587781365	0.00004
NM_000051.4(ATM):c.2159G>A (p.Arg720His)	rs55830714	0.00003
NM_000051.4(ATM):c.2187C>T (p.Tyr729=)	rs373430058	0.00003
NM_000051.4(ATM):c.2449G>C (p.Asp817His)	rs587778067	0.00003
NM_000051.4(ATM):c.2638+9A>G	rs761592414	0.00003
NM_000051.4(ATM):c.2735A>G (p.Gln912Arg)	rs730881353	0.00003
NM_000051.4(ATM):c.2838+9C>G	rs370160823	0.00003
NM_000051.4(ATM):c.3378A>G (p.Lys1126=)	rs149182949	0.00003
NM_000051.4(ATM):c.649A>G (p.Ile217Val)	rs547045780	0.00003
NM_000051.4(ATM):c.6888A>T (p.Ala2296=)	rs200735689	0.00003
NM_000051.4(ATM):c.7618G>A (p.Val2540Ile)	rs35203200	0.00003
NM_000051.4(ATM):c.9006C>T (p.Phe3002=)	rs540172506	0.00003
NM_000051.4(ATM):c.1629T>G (p.Thr543=)	rs760285673	0.00002
NM_000051.4(ATM):c.1648A>G (p.Ile550Val)	rs202144949	0.00002
NM_000051.4(ATM):c.3219A>G (p.Val1073=)	rs752849892	0.00002
NM_000051.4(ATM):c.3963G>A (p.Met1321Ile)	rs35184530	0.00002
NM_000051.4(ATM):c.4050G>A (p.Thr1350=)	rs770697446	0.00002
NM_000051.4(ATM):c.507T>C (p.Ser169=)	rs758619186	0.00002
NM_000051.4(ATM):c.5319+7T>A	rs925428128	0.00002
NM_000051.4(ATM):c.5753G>C (p.Arg1918Thr)	rs148064985	0.00002
NM_000051.4(ATM):c.1444A>C (p.Lys482Gln)	rs202173660	0.00001
NM_000051.4(ATM):c.1494G>A (p.Glu498=)	rs763108858	0.00001
NM_000051.4(ATM):c.2577C>T (p.Asn859=)	rs730881286	0.00001
NM_000051.4(ATM):c.2838+4A>G	rs876659907	0.00001
NM_000051.4(ATM):c.3336T>A (p.Pro1112=)	rs758784434	0.00001
NM_000051.4(ATM):c.372C>A (p.Ile124=)	rs773495195	0.00001
NM_000051.4(ATM):c.4492T>C (p.Leu1498=)	rs748949478	0.00001
NM_000051.4(ATM):c.5319+3C>A	rs371640963	0.00001
NM_000051.4(ATM):c.5320-10T>C	rs864622731	0.00001
NM_000051.4(ATM):c.5488A>G (p.Met1830Val)	rs587781622	0.00001
NM_000051.4(ATM):c.6154G>A (p.Glu2052Lys)	rs202206540	0.00001
NM_000051.4(ATM):c.7328G>A (p.Arg2443Gln)	rs587782310	0.00001
NM_000051.4(ATM):c.7522G>A (p.Gly2508Arg)	rs754395517	0.00001
NM_000051.4(ATM):c.7630-2A>C	rs587779866	0.00001
NM_000051.4(ATM):c.8532T>C (p.Ile2844=)	rs730881278	0.00001
NM_000051.4(ATM):c.858A>G (p.Gln286=)	rs145301478	0.00001
NM_000051.4(ATM):c.8850+10T>C	rs762487236	0.00001
NM_000051.4(ATM):c.8987+3G>A	rs56360226	0.00001
NM_000051.4(ATM):c.-30-5dup	rs745673370
NM_000051.4(ATM):c.156A>C (p.Gly52=)	rs876660725
NM_000051.4(ATM):c.2250+7G>A	rs752009031
NM_000051.4(ATM):c.2251-7A>G	rs879254103
NM_000051.4(ATM):c.3245_3247delinsTGAT (p.His1082fs)	rs587776549
NM_000051.4(ATM):c.4804_4805del (p.Val1602fs)	rs864622290
NM_000051.4(ATM):c.5675-4T>A	rs56075338
NM_000051.4(ATM):c.6998C>A (p.Thr2333Lys)	rs150503164
NM_000051.4(ATM):c.6998C>T (p.Thr2333Ile)	rs150503164
NM_000051.4(ATM):c.7158A>G (p.Ala2386=)	rs2136414393
NM_000051.4(ATM):c.7638_7646del (p.Arg2547_Ser2549del)	rs587776547
NM_000051.4(ATM):c.8269-10_8269-9del	rs587780641
NM_000051.4(ATM):c.8565_8566delinsAA (p.Ser2855_Val2856delinsArgIle)	rs587781353
NM_000051.4(ATM):c.8823_8824del (p.Gln2942fs)	rs1555143538

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