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:
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
65 87 0 46 27 0 19 89

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 8 3 0 0
likely pathogenic 21 0 7 0 0
uncertain significance 2 8 0 6 0
likely benign 0 0 15 0 9
benign 0 0 6 8 0

Submitter to submitter summary #

Total submitters: 23
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
Invitae 0 116 0 27 7 0 12 46
Illumina Laboratory Services, Illumina 0 21 0 3 8 0 1 12
OMIM 0 9 0 4 3 0 2 9
Counsyl 0 9 0 5 0 0 3 8
Natera, Inc. 0 25 0 4 2 0 1 7
Genome-Nilou Lab 0 18 0 5 1 0 1 7
Baylor Genetics 0 13 0 2 1 0 2 5
Revvity Omics, Revvity 0 3 0 1 1 0 2 4
Mendelics 0 7 0 1 0 0 2 3
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 0 0 0 3 0 0 3
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 0 0 2 0 0 0 2
Fulgent Genetics, Fulgent Genetics 0 9 0 1 1 0 0 2
Pars Genome Lab 0 0 0 1 0 0 1 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 0 0 1 0 0 0 1
Intergen, Intergen Genetics and Rare Diseases Diagnosis Center 0 0 0 1 0 0 0 1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 2 0 1 0 0 0 1
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 0 0 1 0 0 0 1
New York Genome Center 0 0 0 0 1 0 0 1
3billion 0 2 0 0 0 0 1 1
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 2 0 0 0 0 1 1
DASA 0 0 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 3 0 0 0 0 1 1
Cowan and Puck Lab, Allergy Immunology and BMT Division, UCSF Benioff Children's Hospital 0 1 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 89
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 0.02676
NM_001033855.3(DCLRE1C):c.959C>G (p.Ser320Cys) rs41298896 0.01123
NM_001033855.3(DCLRE1C):c.457G>A (p.Gly153Arg) rs41297018 0.00964
NM_000215.4(JAK3):c.2164G>A (p.Val722Ile) rs3213409 0.00743
NM_000215.4(JAK3):c.452C>G (p.Pro151Arg) rs55778349 0.00647
NM_000022.4(ADA):c.425G>A (p.Arg142Gln) rs61732239 0.00399
NM_002185.5(IL7R):c.1231A>G (p.Thr411Ala) rs115316501 0.00398
NM_002185.5(IL7R):c.132C>T (p.Ser44=) rs11567704 0.00357
NM_001033855.3(DCLRE1C):c.1284A>C (p.Lys428Asn) rs113870881 0.00220
NM_000022.4(ADA):c.402C>T (p.Gly134=) rs146921882 0.00153
NM_000215.4(JAK3):c.3268G>A (p.Ala1090Thr) rs144968714 0.00150
NM_002185.5(IL7R):c.778G>A (p.Ala260Thr) rs147153824 0.00144
NM_002185.5(IL7R):c.339A>C (p.Glu113Asp) rs11567735 0.00125
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_001033855.3(DCLRE1C):c.419C>T (p.Ala140Val) rs41297016 0.00056
NM_001033855.3(DCLRE1C):c.1791C>T (p.Cys597=) rs115421695 0.00051
NM_002185.5(IL7R):c.152C>T (p.Ser51Leu) rs138482569 0.00047
NM_000215.4(JAK3):c.187A>G (p.Ile63Val) rs144405201 0.00026
NM_000022.4(ADA):c.986C>T (p.Ala329Val) rs121908715 0.00021
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_000022.4(ADA):c.591T>A (p.His197Gln) rs142456343 0.00014
NM_000215.4(JAK3):c.896T>C (p.Val299Ala) rs571404212 0.00012
NM_002185.5(IL7R):c.314G>A (p.Ser105Asn) rs150051812 0.00012
NM_000215.4(JAK3):c.649G>A (p.Val217Met) rs202167678 0.00011
NM_000022.4(ADA):c.192G>A (p.Lys64=) rs144168646 0.00009
NM_000022.4(ADA):c.632G>A (p.Arg211His) rs121908716 0.00009
NM_000215.4(JAK3):c.362G>A (p.Arg121His) rs143586866 0.00008
NM_000022.4(ADA):c.446G>A (p.Arg149Gln) rs121908737 0.00006
NM_000022.4(ADA):c.757C>T (p.Arg253Trp) rs201944717 0.00005
NM_000206.3(IL2RG):c.332T>C (p.Ile111Thr) rs778229878 0.00005
NM_000206.3(IL2RG):c.1105A>G (p.Thr369Ala) rs374270413 0.00004
NM_002185.5(IL7R):c.353G>A (p.Cys118Tyr) rs193922641 0.00004
NM_000022.4(ADA):c.715G>A (p.Gly239Ser) rs777820729 0.00003
NM_000536.4(RAG2):c.217C>T (p.Arg73Cys) rs193922574 0.00003
NM_000022.4(ADA):c.454C>A (p.Leu152Met) rs121908728 0.00002
NM_000206.3(IL2RG):c.1061A>G (p.His354Arg) rs771221019 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.845G>A (p.Arg282Gln) rs751635016 0.00001
NM_000022.4(ADA):c.941A>G (p.Asp314Gly) rs547569818 0.00001
NM_000206.3(IL2RG):c.311A>T (p.His104Leu) rs770804846 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_001033855.3(DCLRE1C):c.47T>C (p.Ile16Thr) rs1317003987 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
NM_000022.4(ADA):c.1078+2T>C
NM_000022.4(ADA):c.201C>G (p.Tyr67Ter) rs1419063255
NM_000022.4(ADA):c.219-2A>G rs387906267
NM_000022.4(ADA):c.396dup (p.Val133fs) rs1555844617
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.703C>T (p.Arg235Trp) rs778809577
NM_000022.4(ADA):c.736C>T (p.Gln246Ter) rs1555844120
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.694G>A (p.Gly232Arg) rs1569479909
NM_000206.3(IL2RG):c.924G>A (p.Ser308=) rs2092255386
NM_000215.4(JAK3):c.1744C>T (p.Arg582Trp) rs193922361
NM_000215.4(JAK3):c.175A>T (p.Lys59Ter)
NM_000215.4(JAK3):c.1915-1G>A
NM_000215.4(JAK3):c.2680+89G>A
NM_000215.4(JAK3):c.2773C>A (p.Arg925Ser) rs149452625
NM_000215.4(JAK3):c.938G>A (p.Gly313Glu) rs200319694
NM_001033855.3(DCLRE1C):c.140T>A (p.Leu47Ter)
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)
NM_001033855.3(DCLRE1C):c.406G>A (p.Asp136Asn) rs1839765652
NM_001033855.3(DCLRE1C):c.82G>C (p.Ala28Pro)
NM_001033855.3(DCLRE1C):c.95C>G (p.Ser32Cys)
NM_001033855.3(DCLRE1C):c.95C>T (p.Ser32Phe) rs969498121
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

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