ClinVar Miner

Variants from ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen with conflicting interpretations

Location: United States  Primary collection method: curation
Minimum review status of the submission from ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen: Collection method of the submission from ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

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
121 180 0 77 38 0 29 139

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 submitters
ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 16 4 0 0
likely pathogenic 39 0 11 0 0
uncertain significance 4 12 0 9 1
likely benign 0 0 22 0 13
benign 0 0 6 9 0

Submitter to submitter summary #

Total submitters: 31
Download table as spreadsheet
Submitter 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
Labcorp Genetics (formerly Invitae), Labcorp 0 198 0 46 12 0 18 76
Illumina Laboratory Services, Illumina 0 26 0 4 12 0 0 16
Natera, Inc. 0 65 0 8 4 0 3 15
OMIM 0 18 0 6 3 0 2 11
Counsyl 0 19 0 5 0 0 5 10
Genome-Nilou Lab 0 22 0 7 1 0 1 9
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 10 0 9 0 0 0 9
Baylor Genetics 0 19 0 3 2 0 2 7
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 0 0 0 4 0 1 5
Fulgent Genetics, Fulgent Genetics 0 12 0 3 1 0 0 4
Revvity Omics, Revvity 0 5 0 1 1 0 2 4
3billion 0 2 0 1 0 0 2 3
Mendelics 0 7 0 1 0 0 2 3
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 0 0 2 0 0 0 2
Department of Pathology and Laboratory Medicine, Sinai Health System 0 3 0 0 1 0 1 2
Pars Genome Lab 0 0 0 1 0 0 1 2
Cowan and Puck Lab, Allergy Immunology and BMT Division, UCSF Benioff Children's Hospital 0 1 0 1 0 0 0 1
First Genomix Gene Laboratory, Genetic Diagnostics Department 0 0 0 0 0 0 1 1
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 4 0 0 0 0 1 1
Intergen Genetics and Rare Diseases Diagnosis Center 0 0 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 4 0 0 0 0 1 1
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 0 0 1 0 0 0 1
Laboratory of Hereditary Immune Disorders, Research Centre for Medical Genetics 0 0 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 1 0 1 0 0 0 1
Laboratory of Pediatric Immunoinfectivology, Tor Vergata University 0 0 0 1 0 0 0 1
Myriad Genetics, Inc. 0 2 0 1 0 0 0 1
Neonatology Unit, University Hospital of Modena 0 0 0 0 0 0 1 1
Neuberg Centre For Genomic Medicine, NCGM 0 2 0 0 0 0 1 1
New York Genome Center 0 0 0 0 1 0 0 1
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 1 0 1 0 0 0 1
van Oers lab, UT Southwestern Medical Center 0 1 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 139
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_002185.5(IL7R):c.412G>A (p.Val138Ile) rs1494555 0.72524
NM_002185.5(IL7R):c.197T>C (p.Ile66Thr) rs1494558 0.68368
NM_000022.4(ADA):c.239A>G (p.Lys80Arg) rs11555566 0.05947
NM_000215.4(JAK3):c.394C>A (p.Pro132Thr) rs3212723 0.02493
NM_001033855.3(DCLRE1C):c.959C>G (p.Ser320Cys) rs41298896 0.01123
NM_001033855.3(DCLRE1C):c.457G>A (p.Gly153Arg) rs41297018 0.00940
NM_000215.4(JAK3):c.2164G>A (p.Val722Ile) rs3213409 0.00743
NM_000215.4(JAK3):c.452C>G (p.Pro151Arg) rs55778349 0.00640
NM_002185.5(IL7R):c.1231A>G (p.Thr411Ala) rs115316501 0.00398
NM_000022.4(ADA):c.425G>A (p.Arg142Gln) rs61732239 0.00376
NM_002185.5(IL7R):c.132C>T (p.Ser44=) rs11567704 0.00357
NM_001033855.3(DCLRE1C):c.1284A>C (p.Lys428Asn) rs113870881 0.00202
NM_001369369.1(FOXN1):c.382C>T (p.Arg128Trp) rs144301161 0.00190
NM_001369369.1(FOXN1):c.1556T>A (p.Leu519Gln) rs34814444 0.00184
NM_000215.4(JAK3):c.3268G>A (p.Ala1090Thr) rs144968714 0.00150
NM_000022.4(ADA):c.402C>T (p.Gly134=) rs146921882 0.00139
NM_002185.5(IL7R):c.778G>A (p.Ala260Thr) rs147153824 0.00130
NM_002185.5(IL7R):c.339A>C (p.Glu113Asp) rs11567735 0.00119
NM_002185.5(IL7R):c.1020T>G (p.Leu340=) rs138731184 0.00096
NM_000206.3(IL2RG):c.325G>A (p.Glu109Lys) rs17875899 0.00059
NM_001369369.1(FOXN1):c.1184C>T (p.Pro395Leu) rs199739943 0.00056
NM_001033855.3(DCLRE1C):c.419C>T (p.Ala140Val) rs41297016 0.00054
NM_000215.4(JAK3):c.2152G>C (p.Val718Leu) rs146837396 0.00052
NM_001033855.3(DCLRE1C):c.1791C>T (p.Cys597=) rs115421695 0.00048
NM_002185.5(IL7R):c.152C>T (p.Ser51Leu) rs138482569 0.00042
NM_000215.4(JAK3):c.187A>G (p.Ile63Val) rs144405201 0.00023
NM_002185.5(IL7R):c.707G>A (p.Gly236Glu) rs201084372 0.00021
NM_000022.4(ADA):c.930G>A (p.Met310Ile) rs145924854 0.00019
NM_000022.4(ADA):c.986C>T (p.Ala329Val) rs121908715 0.00019
NM_002185.5(IL7R):c.602A>G (p.Tyr201Cys) rs145810271 0.00017
NM_001033855.3(DCLRE1C):c.169G>T (p.Val57Phe) rs138077101 0.00016
NM_001369369.1(FOXN1):c.1886C>T (p.Thr629Met) rs368962978 0.00016
NM_002185.5(IL7R):c.314G>A (p.Ser105Asn) rs150051812 0.00016
NM_000022.4(ADA):c.192G>A (p.Lys64=) rs144168646 0.00015
NM_000022.4(ADA):c.591T>A (p.His197Gln) rs142456343 0.00013
NM_000215.4(JAK3):c.896T>C (p.Val299Ala) rs571404212 0.00012
NM_001369369.1(FOXN1):c.1664C>T (p.Ala555Val) rs187814037 0.00012
NM_000215.4(JAK3):c.649G>A (p.Val217Met) rs202167678 0.00011
NM_000215.4(JAK3):c.938G>A (p.Gly313Glu) rs200319694 0.00010
NR_003051.4(RMRP):n.244A>G rs551450545 0.00010
NM_000022.4(ADA):c.632G>A (p.Arg211His) rs121908716 0.00009
NM_000215.4(JAK3):c.362G>A (p.Arg121His) rs143586866 0.00009
NM_000022.4(ADA):c.446G>A (p.Arg149Gln) rs121908737 0.00006
NM_000022.4(ADA):c.872C>T (p.Ser291Leu) rs121908721 0.00005
NM_000206.3(IL2RG):c.1105A>G (p.Thr369Ala) rs374270413 0.00005
NM_000206.3(IL2RG):c.332T>C (p.Ile111Thr) rs778229878 0.00005
NM_002185.5(IL7R):c.539A>C (p.His180Pro) rs193922642 0.00005
NR_003051.4(RMRP):n.37C>A rs549085067 0.00005
NM_001369369.1(FOXN1):c.124-17A>T rs376727518 0.00004
NM_000022.4(ADA):c.715G>A (p.Gly239Ser) rs777820729 0.00003
NM_000206.3(IL2RG):c.1061A>G (p.His354Arg) rs771221019 0.00003
NM_000536.4(RAG2):c.217C>T (p.Arg73Cys) rs193922574 0.00003
NM_001369369.1(FOXN1):c.1706C>A (p.Ser569Tyr) rs149225004 0.00003
NM_000022.4(ADA):c.454C>A (p.Leu152Met) rs121908728 0.00002
NM_000022.4(ADA):c.911T>G (p.Leu304Arg) rs199422327 0.00002
NM_000022.4(ADA):c.941A>G (p.Asp314Gly) rs547569818 0.00002
NM_000206.3(IL2RG):c.1076C>T (p.Ala359Val) rs767383120 0.00002
NM_000206.3(IL2RG):c.292A>G (p.Lys98Glu) rs776710796 0.00002
NM_000206.3(IL2RG):c.963G>A (p.Leu321=) rs181901993 0.00002
NM_000215.4(JAK3):c.1843C>T (p.Arg615Cys) rs200075643 0.00002
NM_000022.4(ADA):c.445C>T (p.Arg149Trp) rs121908733 0.00001
NM_000022.4(ADA):c.631C>T (p.Arg211Cys) rs121908740 0.00001
NM_000022.4(ADA):c.703C>T (p.Arg235Trp) rs778809577 0.00001
NM_000022.4(ADA):c.845G>A (p.Arg282Gln) rs751635016 0.00001
NM_000206.3(IL2RG):c.311A>T (p.His104Leu) rs770804846 0.00001
NM_000206.3(IL2RG):c.348G>T (p.Gln116His) rs778547446 0.00001
NM_000206.3(IL2RG):c.406C>T (p.Arg136Trp) rs758080286 0.00001
NM_000206.3(IL2RG):c.924+9G>T rs1198550634 0.00001
NM_000206.3(IL2RG):c.977G>A (p.Ser326Asn) rs779190567 0.00001
NM_000215.4(JAK3):c.1744C>T (p.Arg582Trp) rs193922361 0.00001
NM_000215.4(JAK3):c.2323C>T (p.Arg775Cys) rs200624610 0.00001
NM_000215.4(JAK3):c.578G>A (p.Cys193Tyr) rs1467075214 0.00001
NM_001033855.3(DCLRE1C):c.291T>C (p.Asp97=) rs1840574128 0.00001
NM_001033855.3(DCLRE1C):c.47T>C (p.Ile16Thr) rs1317003987 0.00001
NM_001033855.3(DCLRE1C):c.572G>A (p.Arg191Gln) rs528699445 0.00001
NM_001369369.1(FOXN1):c.1049C>T (p.Pro350Leu) rs771407322 0.00001
NM_001369369.1(FOXN1):c.958C>T (p.Arg320Trp) rs1288977950 0.00001
NM_002185.5(IL7R):c.265C>T (p.Gln89Ter) rs141698985 0.00001
NM_002185.5(IL7R):c.83-2A>T rs886060531 0.00001
NR_003051.4(RMRP):n.195G>A rs761398394 0.00001
NR_003051.4(RMRP):n.232C>T rs762145032 0.00001
NC_000009.12:g.35657872C>T rs753874439
NM_000022.4(ADA):c.1078+2T>C rs1555843178
NM_000022.4(ADA):c.201C>G (p.Tyr67Ter) rs1419063255
NM_000022.4(ADA):c.219-2A>G rs387906267
NM_000022.4(ADA):c.311C>T (p.Pro104Leu) rs1452483770
NM_000022.4(ADA):c.396dup (p.Val133fs) rs1555844617
NM_000022.4(ADA):c.516C>A (p.Tyr172Ter) rs748810619
NM_000022.4(ADA):c.532del (p.Val177_Val178insTer) rs886041796
NM_000022.4(ADA):c.603C>A (p.Tyr201Ter) rs1555844395
NM_000022.4(ADA):c.603C>G (p.Tyr201Ter) rs1555844395
NM_000022.4(ADA):c.716G>A (p.Gly239Asp) rs1312320956
NM_000022.4(ADA):c.736C>T (p.Gln246Ter) rs1555844120
NM_000206.3(IL2RG):c.100G>T (p.Glu34Ter) rs1556331272
NM_000206.3(IL2RG):c.175G>T (p.Glu59Ter) rs2092262517
NM_000206.3(IL2RG):c.181C>T (p.Gln61Ter) rs1569480082
NM_000206.3(IL2RG):c.216C>A (p.Cys72Ter) rs2147750927
NM_000206.3(IL2RG):c.43C>T (p.Gln15Ter) rs1057517747
NM_000206.3(IL2RG):c.455T>G (p.Val152Gly) rs193922348
NM_000206.3(IL2RG):c.694G>A (p.Gly232Arg) rs1569479909
NM_000206.3(IL2RG):c.710G>A (p.Trp237Ter) rs193922350
NM_000206.3(IL2RG):c.924G>A (p.Ser308=) rs2092255386
NM_000206.3(IL2RG):c.982C>T (p.Arg328Ter) rs1064793347
NM_000215.4(JAK3):c.1333C>T (p.Arg445Ter) rs137852626
NM_000215.4(JAK3):c.175A>T (p.Lys59Ter) rs2514582034
NM_000215.4(JAK3):c.1915-1G>A rs1449943380
NM_000215.4(JAK3):c.2680+89G>A rs2514549046
NM_000215.4(JAK3):c.2773C>A (p.Arg925Ser) rs149452625
NM_001033855.3(DCLRE1C):c.140T>A (p.Leu47Ter) rs2492399920
NM_001033855.3(DCLRE1C):c.1669dup (p.Thr557fs) rs886037924
NM_001033855.3(DCLRE1C):c.180C>A (p.Tyr60Ter) rs2131108640
NM_001033855.3(DCLRE1C):c.206T>A (p.Leu69Ter) rs1589136659
NM_001033855.3(DCLRE1C):c.346T>C (p.Cys116Arg) rs2492076708
NM_001033855.3(DCLRE1C):c.406G>A (p.Asp136Asn) rs1839765652
NM_001033855.3(DCLRE1C):c.82G>C (p.Ala28Pro) rs773046452
NM_001369369.1(FOXN1):c.1010del (p.Gly337fs) rs2151497970
NM_001369369.1(FOXN1):c.1275_1278del (p.Leu426fs)
NM_001369369.1(FOXN1):c.1315del (p.Leu439fs) rs1064796227
NM_001369369.1(FOXN1):c.1364_1367del (p.Tyr455fs) rs2151499024
NM_001369369.1(FOXN1):c.1367T>A (p.Leu456Ter) rs2508429713
NM_001369369.1(FOXN1):c.1392_1401del (p.Pro465fs) rs1597567985
NM_001369369.1(FOXN1):c.1465del (p.Gln489fs) rs1169577591
NM_001369369.1(FOXN1):c.1585del (p.Leu529fs) rs1161194345
NM_001369369.1(FOXN1):c.362C>T (p.Ala121Val) rs557541901
NM_001369369.1(FOXN1):c.699+1G>T rs1555609768
NM_001369369.1(FOXN1):c.880G>A (p.Val294Ile)
NM_001369369.1(FOXN1):c.880G>C (p.Val294Leu) rs1406320425
NM_001369369.1(FOXN1):c.928-2A>G rs2151497815
NM_001369369.1(FOXN1):c.974T>C (p.Leu325Pro) rs1597566470
NM_002185.5(IL7R):c.135G>C (p.Gln45His) rs200464578
NM_002185.5(IL7R):c.235G>T (p.Glu79Ter) rs1354581284
NM_002185.5(IL7R):c.355A>T (p.Lys119Ter) rs1448018291
NM_002185.5(IL7R):c.394C>T (p.Pro132Ser) rs104893894
NM_002185.5(IL7R):c.41T>C (p.Leu14Ser) rs1759661333
NM_002185.5(IL7R):c.704C>G (p.Ser235Ter) rs766555082
NM_002185.5(IL7R):c.82+14A>T rs1038024322
NR_003051.4(RMRP):n.-24_-3dup rs1554651423
NR_003051.4(RMRP):n.220A>G rs936059863
NR_003051.4(RMRP):n.244A>C rs551450545

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