ClinVar Miner

Variants with conflicting interpretations studied for Severe Combined Immune Deficiency

Coded as:
Minimum review status of the submission for Severe Combined Immune Deficiency: Y axis collection method of the submission for Severe Combined Immune Deficiency:
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 Variants with at least 2 submissions 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 kind of conflict
148 93 1 19 16 0 2 37

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
Severe Combined Immune Deficiency likely pathogenic uncertain significance likely benign benign
uncertain significance 1 1 7 8
likely benign 1 0 0 18
benign 0 2 1 0

Condition to condition summary #

Total conditions: 12
Download table as spreadsheet
Condition Variants with only 1 submission Variants with at least 2 submissions 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 kind of conflict
not specified 0 19 0 13 2 0 0 15
Combined cellular and humoral immune defects with granulomas; Severe immunodeficiency, autosomal recessive, T-cell negative, B-cell negative, NK cell-positive 0 2 0 6 3 0 0 9
Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-negative 0 2 0 2 5 0 0 7
Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive 0 2 0 3 2 0 0 5
Immunodeficiency 18 0 2 0 1 3 0 0 4
Severe combined immunodeficiency disease 0 1 1 1 1 0 1 4
not provided 0 3 0 3 1 0 0 4
Severe combined immunodeficiency, atypical 0 1 0 2 1 0 0 3
Acute megakaryoblastic leukemia 0 0 0 0 0 0 1 1
Immunodeficiency due to defect in CD3-gamma 0 0 0 1 0 0 0 1
Lymphoblastic leukemia, acute, with lymphomatous features 0 0 0 0 0 0 1 1
X-linked severe combined immunodeficiency 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 37
Download table as spreadsheet
HGVS dbSNP
NM_000073.2(CD3G):c.-46_-43delGCTG rs60810919
NM_000206.2(IL2RG):c.325G>A (p.Glu109Lys) rs17875899
NM_000215.3(JAK3):c.1548C>T (p.Ile516=) rs144203232
NM_000215.3(JAK3):c.187A>G (p.Ile63Val) rs144405201
NM_000215.3(JAK3):c.1929G>A (p.Leu643=) rs138645044
NM_000215.3(JAK3):c.2062A>T (p.Ile688Phe) rs35785705
NM_000215.3(JAK3):c.2152G>C (p.Val718Leu) rs146837396
NM_000215.3(JAK3):c.2451C>T (p.Phe817=) rs201576913
NM_000215.3(JAK3):c.297G>C (p.Leu99=) rs3212716
NM_000215.3(JAK3):c.394C>A (p.Pro132Thr) rs3212723
NM_000448.2(RAG1):c.189A>G (p.Pro63=) rs34357808
NM_000448.2(RAG1):c.2659G>A (p.Asp887Asn) rs4151034
NM_000448.2(RAG1):c.2880A>G (p.Ala960=) rs1980131
NM_000448.2(RAG1):c.303G>A (p.Ala101=) rs4151025
NM_000448.2(RAG1):c.577G>A (p.Glu193Lys) rs34841221
NM_000448.2(RAG1):c.906C>A (p.Asp302Glu) rs4151030
NM_000536.3(RAG2):c.*52T>A rs546979744
NM_000536.3(RAG2):c.1095T>C (p.Ser365=) rs140519815
NM_000536.3(RAG2):c.22G>A (p.Val8Ile) rs150762709
NM_000536.3(RAG2):c.741G>A (p.Val247=) rs34092949
NM_000536.3(RAG2):c.878A>G (p.Glu293Gly) rs16929093
NM_000733.3(CD3E):c.*98_*101dupAATC rs193922618
NM_000733.3(CD3E):c.103C>T (p.Pro35Ser) rs143949187
NM_000733.3(CD3E):c.211G>C (p.Asp71His) rs148647954
NM_000733.3(CD3E):c.216T>C (p.Asp72=) rs2231444
NM_000733.3(CD3E):c.507C>T (p.Gly169=) rs2231447
NM_001079.3(ZAP70):c.105G>A (p.Leu35=) rs56127120
NM_001079.3(ZAP70):c.447G>A (p.Val149=) rs61735392
NM_001079.3(ZAP70):c.672C>T (p.Pro224=) rs56340622
NM_002185.3(IL7R):c.197T>C (p.Ile66Thr) rs1494558
NM_002185.3(IL7R):c.412G>A (p.Val138Ile) rs1494555
NM_002185.3(IL7R):c.495C>T (p.His165=) rs2228141
NM_002185.3(IL7R):c.538-14A>C rs11567763
NM_002185.4(IL7R):c.1241C>T (p.Thr414Met) rs2229232
NM_002185.4(IL7R):c.153G>A (p.Ser51=) rs149235072
NM_002185.4(IL7R):c.214G>C (p.Glu72Gln) rs148001159
NM_002185.4(IL7R):c.561G>A (p.Lys187=) rs11567764

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