Total 17 pathogenic variants reported for Common variable immunodeficiency 
Variant Name Variant Type Variant Genomic Location Clinical Significance Phenotype Condition Review Status ClinGen Allele dbSNP ID Variation/condition record
NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg) SNV
Germline		 Chr17:16948873 Conflicting classifications of pathogenicity; risk factor Immunoglobulin A deficiency 2
Immunodeficiency, common variable, 2
Common Variable Immune Deficiency, Dominant
Condition: not provided
not specified
16 conditions
Common variable immunodeficiency
Immunodeficiency, common variable, 2
Immunodeficiency, common variable, 1
Immunodeficiency, common variable, 1
Immunodeficiency, common variable, 2
Immunoglobulin A deficiency 2
Severe SARS-CoV-2 infection, susceptibility to
TNFRSF13B-related disorder
Immune deficiency, familial variable		 Criteria Provided
Conflicting Classifications
 CA117387 rs_34557412

41 SubmittersRCV000005624RCV000005623RCV000302082RCV000403933RCV000507544RCV000735370RCV001526850RCV001535526RCV002283439RCV002054418RCV001374734RCV003398448RCV003448244
NM_012452.3(TNFRSF13B):c.542C>A (p.Ala181Glu) SNV
Germline		 Chr17:16940415 Conflicting classifications of pathogenicity Immunodeficiency, common variable, 2
Immunoglobulin A deficiency 2
Condition: not provided
not specified
Common variable immunodeficiency
Immunodeficiency, common variable, 2
Immunoglobulin A deficiency 2
See cases		 Criteria Provided
Conflicting Classifications
 CA117389 rs_72553883

24 SubmittersRCV000005625RCV000005626RCV000255118RCV000999848RCV001199863RCV002054419RCV002251881
NM_000536.4(RAG2):c.1352G>C (p.Gly451Ala) SNV
Germline		 Chr11:36592817 Pathogenic Combined immunodeficiency with skin granulomas
Condition: not provided
Combined immunodeficiency with skin granulomas
Recombinase activating gene 2 deficiency
Inborn error of immunity
Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive
Combined immunodeficiency with skin granulomas
Common variable immunodeficiency
Severe combined immunodeficiency disease
Recombinase activating gene 2 deficiency		 Reviewed By Expert Panel
 CA122872 rs_121918575

9 SubmittersRCV000014020RCV000521152RCV000681597RCV000821298RCV001027616RCV001731284RCV003398501
NM_001322934.2(NFKB2):c.2557C>T (p.Arg853Ter) SNV
Germline		 Chr10:102402138 Pathogenic not specified
Immunodeficiency, common variable, 10
Inherited Immunodeficiency Diseases
Condition: not provided
Common variable immunodeficiency		 Criteria Provided
Multiple Submitters
No Conflicts
 CA144753 rs_397514332

13 SubmittersRCV000055612RCV000077761RCV001027606RCV001093426RCV001174741
NM_012452.3(TNFRSF13B):c.260T>A (p.Ile87Asn) SNV
Germline		 Chr17:16948923 Conflicting classifications of pathogenicity Condition: not provided
Immunodeficiency, common variable, 2
Common variable immunodeficiency
Immunodeficiency, common variable, 2
IgAD1		 Criteria Provided
Conflicting Classifications
 rs_72553877

9 SubmittersRCV000756794RCV000800201RCV001844233RCV002508946
NM_003809.3(TNFSF12):c.674G>A (p.Arg225Gln) SNV
Germline		 Chr17:7557274 Conflicting classifications of pathogenicity Condition: not provided
TNFSF12-related disorder
Common variable immunodeficiency		 Criteria Provided
Conflicting Classifications
 rs_576689580

3 SubmittersRCV000762199RCV003413552RCV001855950
NM_020458.4(TTC7A):c.793C>T (p.Arg265Trp) SNV
Germline		 Chr2:46993478 Conflicting classifications of pathogenicity Common variable immunodeficiency
Multiple gastrointestinal atresias
not specified		 Criteria Provided
Conflicting Classifications
 rs_150269540

3 SubmittersRCV001027641RCV001367045RCV004526797
NM_003998.4(NFKB1):c.260T>G (p.Ile87Ser) SNV
Germline		 Chr4:102566988 Pathogenic Common variable immunodeficiency
Immunodeficiency, common variable, 12		 Criteria Provided
Single Submitter
 rs_1578771120

2 SubmittersRCV001027589RCV001374707
NM_003998.4(NFKB1):c.293T>A (p.Val98Asp) SNV
Germline		 Chr4:102567021 Pathogenic Common variable immunodeficiency Criteria Provided
Single Submitter
 rs_1578771197

1 SubmittersRCV001027591
NM_003998.4(NFKB1):c.843C>G (p.Ile281Met) SNV
Germline		 Chr4:102582873 Pathogenic Common variable immunodeficiency Criteria Provided
Single Submitter
 rs_1578793298

1 SubmittersRCV001027592
NM_003998.4(NFKB1):c.850C>T (p.Arg284Ter) SNV
Germline		 Chr4:102582880 Pathogenic/Likely pathogenic Common variable immunodeficiency
Inherited Immunodeficiency Diseases
Immunodeficiency, common variable, 12
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 rs_1578793312

4 SubmittersRCV001027598RCV001027604RCV001262753RCV002552007
NM_000536.4(RAG2):c.629T>C (p.Ile210Thr) SNV
Germline		 Chr11:36593540 Pathogenic Common variable immunodeficiency Criteria Provided
Single Submitter
 rs_1590715754

1 SubmittersRCV001027617
NM_020458.4(TTC7A):c.1802+3G>C SNV
Germline		 Chr2:47029387 Conflicting classifications of pathogenicity Common variable immunodeficiency
Multiple gastrointestinal atresias
not specified		 Criteria Provided
Conflicting Classifications
 rs_1572961263

3 SubmittersRCV001027636RCV001862411RCV003230621
NM_012452.3(TNFRSF13B):c.61+2T>A SNV
Germline		 Chr17:16972013 Pathogenic Immunodeficiency, common variable, 2
Common variable immunodeficiency		 Criteria Provided
Single Submitter
 rs_760885614

2 SubmittersRCV001212531RCV003493823
NM_003998.4(NFKB1):c.1753-1G>C SNV
Germline		 Chr4:102606495 Likely pathogenic Condition: not provided
Common variable immunodeficiency		 Criteria Provided
Multiple Submitters
No Conflicts

2 SubmittersRCV003683733RCV004018000