Total 60 pathogenic variants reported for Acute lymphoid leukemia 
Variant Name Variant Type Variant Genomic Location Clinical Significance Phenotype Condition Review Status ClinGen Allele dbSNP ID Variation/condition record
NM_002485.5(NBN):c.511A>G (p.Ile171Val) SNV
Germline		 Chr8:89978293 Conflicting classifications of pathogenicity Aplastic anemia
Leukemia, acute lymphoblastic, susceptibility to
Hereditary cancer-predisposing syndrome
not specified
Microcephaly, normal intelligence and immunodeficiency
Acute lymphoid leukemia
Condition: not provided
Hereditary breast ovarian cancer syndrome
Breast carcinoma
Carcinoma of colon
Hereditary cancer
NBN-related disorder
Diffuse midline glioma, H3 K27-altered
Pediatric high-grade glioma		 Criteria Provided
Conflicting Classifications
 CA160981 rs_61754966

27 SubmittersRCV000007360RCV000007361RCV000115797RCV000121618RCV000197512RCV000490266RCV000589577RCV001030566RCV001262350RCV001358233RCV003492288RCV003891430RCV004776268RCV004776269
NM_004119.3(FLT3):c.2504A>T (p.Asp835Val) SNV
Somatic		 Chr13:28018504 Pathogenic Acute myeloid leukemia
Acute lymphoid leukemia		 No Assertion Criteria Provided
 CA126344 rs_121909646

1 SubmittersRCV000017660RCV000017661
NM_004119.3(FLT3):c.2503G>T (p.Asp835Tyr) SNV
Somatic		 Chr13:28018505 Pathogenic Acute lymphoid leukemia
Acute myeloid leukemia		 No Assertion Criteria Provided
 CA126347 rs_121913488

2 SubmittersRCV000017666RCV000017665
NM_002485.5(NBN):c.1262T>C (p.Leu421Ser) SNV
Germline		 Chr8:89955418 Conflicting classifications of pathogenicity Aplastic anemia
Acute lymphoid leukemia
Microcephaly, normal intelligence and immunodeficiency
Familial cancer of breast
Malignant tumor of breast
Condition: not provided
Hereditary cancer-predisposing syndrome
Microcephaly, normal intelligence and immunodeficiency
not specified		 Criteria Provided
Conflicting Classifications
 CA230729 rs_104895032

24 SubmittersRCV000515275RCV000757930RCV001358304RCV000114875RCV000115780RCV000123203RCV000212745
NM_002485.5(NBN):c.628G>T (p.Val210Phe) SNV
Germline		 Chr8:89971247 Conflicting classifications of pathogenicity Aplastic anemia
Acute lymphoid leukemia
Microcephaly, normal intelligence and immunodeficiency
Malignant tumor of breast
NBN-related disorder
Condition: not provided
Hereditary cancer-predisposing syndrome
not specified
Microcephaly, normal intelligence and immunodeficiency		 Criteria Provided
Conflicting Classifications
 CA160993 rs_61754796

23 SubmittersRCV000515300RCV001358247RCV003891593RCV000114880RCV000115801RCV000121622RCV000168062
NM_000077.5(CDKN2A):c.146T>C (p.Ile49Thr) SNV
Germline/somatic		 Chr9:21974682 Conflicting classifications of pathogenicity Melanoma-pancreatic cancer syndrome
not specified
Osteoblastic osteosarcoma
Melanoma and neural system tumor syndrome
Melanoma and neural system tumor syndrome
Melanoma-pancreatic cancer syndrome
Acute lymphoid leukemia
CDKN2A-related disorder
Hereditary cancer-predisposing syndrome
Familial melanoma
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA287160 rs_199907548

15 SubmittersRCV000412396RCV001001912RCV000761151RCV001292944RCV001535568RCV003444104RCV003891607RCV000115331RCV000122945RCV000212398
NM_002485.5(NBN):c.1999T>C (p.Ser667Pro) SNV
Germline		 Chr8:89946211 Conflicting classifications of pathogenicity Hereditary cancer-predisposing syndrome
Condition: not provided
Microcephaly, normal intelligence and immunodeficiency
Microcephaly, normal intelligence and immunodeficiency
Acute lymphoid leukemia
Aplastic anemia
Aplastic anemia
not specified
NBN-related disorder		 Criteria Provided
Conflicting Classifications
 CA287913 rs_587780091

13 SubmittersRCV000115786RCV000212753RCV000230585RCV000515337RCV001328956RCV001778709RCV003915124
NM_002485.5(NBN):c.425A>G (p.Asn142Ser) SNV
Germline		 Chr8:89980789 Conflicting classifications of pathogenicity Hereditary cancer-predisposing syndrome
not specified
Microcephaly, normal intelligence and immunodeficiency
Microcephaly, normal intelligence and immunodeficiency
Acute lymphoid leukemia
Aplastic anemia
Condition: not provided
Malignant tumor of breast
Hereditary cancer		 Criteria Provided
Conflicting Classifications
 CA160978 rs_769414

14 SubmittersRCV000115794RCV000121617RCV000168260RCV000515292RCV000589414RCV001355243RCV003492491
NM_002485.5(NBN):c.456G>A (p.Met152Ile) SNV
Germline		 Chr8:89980758 Conflicting classifications of pathogenicity Hereditary cancer-predisposing syndrome
Microcephaly, normal intelligence and immunodeficiency
Condition: not provided
Microcephaly, normal intelligence and immunodeficiency
Acute lymphoid leukemia
Aplastic anemia
not specified
Malignant tumor of breast
Aplastic anemia		 Criteria Provided
Conflicting Classifications
 CA287934 rs_201816949

18 SubmittersRCV000115795RCV000197783RCV000509203RCV000515395RCV000781635RCV001356300RCV003467061
NM_002485.5(NBN):c.505C>T (p.Arg169Cys) SNV
Germline		 Chr8:89978299 Conflicting classifications of pathogenicity Hereditary cancer-predisposing syndrome
Microcephaly, normal intelligence and immunodeficiency
Condition: not provided
Microcephaly, normal intelligence and immunodeficiency
Acute lymphoid leukemia
Aplastic anemia
Hereditary breast ovarian cancer syndrome
not specified
NBN-related disorder		 Criteria Provided
Conflicting Classifications
 CA287937 rs_182756889

13 SubmittersRCV000115796RCV000123218RCV000587269RCV000764786RCV001030567RCV001549273RCV003389690
NM_002485.5(NBN):c.595C>T (p.Pro199Ser) SNV
Germline		 Chr8:89971280 Conflicting classifications of pathogenicity Hereditary cancer-predisposing syndrome
Condition: not provided
Microcephaly, normal intelligence and immunodeficiency
Microcephaly, normal intelligence and immunodeficiency
Acute lymphoid leukemia
Aplastic anemia		 Criteria Provided
Conflicting Classifications
 CA287940 rs_587780097

10 SubmittersRCV000115798RCV000235189RCV000461206RCV000515203
NM_002485.5(NBN):c.1903A>T (p.Lys635Ter) SNV
Germline		 Chr8:89947835 Pathogenic/Likely pathogenic Hereditary cancer-predisposing syndrome
Condition: not provided
Microcephaly, normal intelligence and immunodeficiency
Aplastic anemia
Acute lymphoid leukemia
Microcephaly, normal intelligence and immunodeficiency
Aplastic anemia		 Criteria Provided
Multiple Submitters
No Conflicts
 CA168703 rs_587782545

12 SubmittersRCV000131755RCV000219708RCV000227700RCV000763606RCV003467185
NM_002485.5(NBN):c.2140C>T (p.Arg714Ter) SNV
Germline		 Chr8:89943297 Pathogenic/Likely pathogenic Condition: not provided
Microcephaly, normal intelligence and immunodeficiency
Hereditary cancer-predisposing syndrome
Microcephaly, normal intelligence and immunodeficiency
Acute lymphoid leukemia
Aplastic anemia
Aplastic anemia		 Criteria Provided
Multiple Submitters
No Conflicts
 CA299657 rs_730881864

15 SubmittersRCV000160804RCV000204431RCV000215628RCV000515171RCV003467267
NM_002485.5(NBN):c.1030C>T (p.Gln344Ter) SNV
Germline		 Chr8:89958819 Pathogenic/Likely pathogenic Microcephaly, normal intelligence and immunodeficiency
Condition: not provided
Hereditary cancer-predisposing syndrome
Acute lymphoid leukemia
Microcephaly, normal intelligence and immunodeficiency
Aplastic anemia
Aplastic anemia		 Criteria Provided
Multiple Submitters
No Conflicts
 CA274767 rs_767215758

11 SubmittersRCV000170448RCV000220210RCV000446931RCV000763607RCV003474919
NM_001987.5(ETV6):c.1046T>C (p.Leu349Pro) SNV
Germline		 Chr12:11884481 Likely pathogenic Acute lymphoid leukemia
Thrombocytopenia
Thrombocytopenia
Inborn genetic diseases		 Criteria Provided
Single Submitter
 CA277990 rs_786205155

2 SubmittersRCV000170464RCV000170465RCV004020020
NM_002485.5(NBN):c.1747C>T (p.Gln583Ter) SNV
Germline		 Chr8:89953342 Pathogenic/Likely pathogenic Microcephaly, normal intelligence and immunodeficiency
Hereditary cancer-predisposing syndrome
Condition: not provided
Aplastic anemia
Acute lymphoid leukemia
Microcephaly, normal intelligence and immunodeficiency
Aplastic anemia		 Criteria Provided
Multiple Submitters
No Conflicts
 CA350525 rs_864622143

7 SubmittersRCV000206506RCV000217030RCV001753608RCV002478725RCV003468931
NM_002485.5(NBN):c.897-2A>T SNV
Germline		 Chr8:89964509 Likely pathogenic Microcephaly, normal intelligence and immunodeficiency
Hereditary cancer-predisposing syndrome
Condition: not provided
Aplastic anemia
Acute lymphoid leukemia
Microcephaly, normal intelligence and immunodeficiency
NBN-related disorder
Aplastic anemia		 Criteria Provided
Multiple Submitters
No Conflicts
 CA348947 rs_864622090

9 SubmittersRCV000204744RCV000222760RCV001567181RCV002057048RCV003401102RCV003474977
NM_002485.5(NBN):c.340G>T (p.Val114Phe) SNV
Germline		 Chr8:89980874 Conflicting classifications of pathogenicity Microcephaly, normal intelligence and immunodeficiency
Hereditary cancer-predisposing syndrome
not specified
Aplastic anemia
Acute lymphoid leukemia
Microcephaly, normal intelligence and immunodeficiency
Condition: not provided
Aplastic anemia		 Criteria Provided
Conflicting Classifications
 CA350859 rs_771034958

9 SubmittersRCV000206877RCV000220601RCV000486552RCV000764790RCV000767209RCV003474978
NM_002485.5(NBN):c.265C>T (p.Arg89Ter) SNV
Germline		 Chr8:89981430 Pathogenic/Likely pathogenic Microcephaly, normal intelligence and immunodeficiency
Hereditary cancer-predisposing syndrome
Condition: not provided
Acute lymphoid leukemia
Aplastic anemia
Microcephaly, normal intelligence and immunodeficiency
Gastric cancer
Aplastic anemia		 Criteria Provided
Multiple Submitters
No Conflicts
 CA16041212 rs_1057516320

9 SubmittersRCV000410234RCV001176293RCV001782863RCV002504201RCV003168586RCV003470325
NM_002485.5(NBN):c.1754A>G (p.Glu585Gly) SNV
Germline		 Chr8:89953335 Conflicting classifications of pathogenicity Microcephaly, normal intelligence and immunodeficiency
Hereditary cancer-predisposing syndrome
Condition: not provided
Malignant tumor of breast
not specified
Acute lymphoid leukemia
Aplastic anemia
Microcephaly, normal intelligence and immunodeficiency		 Criteria Provided
Conflicting Classifications
 CA4802685 rs_763926389

9 SubmittersRCV000461649RCV000567576RCV000679454RCV001358087RCV002282161RCV002475888
NM_002485.5(NBN):c.481-2A>T SNV
Germline		 Chr8:89978325 Pathogenic/Likely pathogenic Condition: not provided
Hereditary cancer-predisposing syndrome
Microcephaly, normal intelligence and immunodeficiency
Aplastic anemia
Microcephaly, normal intelligence and immunodeficiency
Acute lymphoid leukemia
Aplastic anemia		 Criteria Provided
Multiple Submitters
No Conflicts
 CA4802955 rs_751567476

9 SubmittersRCV000523496RCV000569604RCV000707500RCV002497023RCV003470656
NM_002485.5(NBN):c.1279C>A (p.Pro427Thr) SNV
Germline		 Chr8:89955401 Conflicting classifications of pathogenicity Hereditary cancer-predisposing syndrome
Microcephaly, normal intelligence and immunodeficiency
Aplastic anemia
Microcephaly, normal intelligence and immunodeficiency
Acute lymphoid leukemia		 Criteria Provided
Conflicting Classifications
 CA371656207 rs_1554559171

4 SubmittersRCV000569911RCV001054209RCV002491138
NM_016734.3(PAX5):c.239C>G (p.Pro80Arg) SNV
Somatic		 Chr9:37015168 Likely pathogenic Acute lymphoid leukemia Criteria Provided
Single Submitter

2 SubmittersRCV000766127
NM_002485.5(NBN):c.390A>G (p.Gln130=) SNV
Germline		 Chr8:89980824 Conflicting classifications of pathogenicity Condition: not provided
Microcephaly, normal intelligence and immunodeficiency
Acute lymphoid leukemia
Aplastic anemia
Microcephaly, normal intelligence and immunodeficiency
Hereditary cancer-predisposing syndrome
not specified		 Criteria Provided
Conflicting Classifications
 rs_146150499

6 SubmittersRCV001619837RCV000768028RCV000799906RCV001021414RCV002271580
NM_002485.5(NBN):c.1106C>G (p.Ser369Ter) SNV
Germline		 Chr8:89958743 Pathogenic/Likely pathogenic Microcephaly, normal intelligence and immunodeficiency
Acute lymphoid leukemia
Microcephaly, normal intelligence and immunodeficiency
Aplastic anemia
Aplastic anemia
Hereditary cancer-predisposing syndrome		 Criteria Provided
Multiple Submitters
No Conflicts
 rs_2129744741

4 SubmittersRCV001386835RCV002476731RCV003469725RCV004037684
NM_006060.6(IKZF1):c.530T>C (p.Leu177Pro) SNV
Somatic		 Chr7:50382648 Likely pathogenic Pancytopenia due to IKZF1 mutations
Acute lymphoid leukemia		 Criteria Provided
Multiple Submitters
No Conflicts
 rs_2153477847

2 SubmittersRCV001706897RCV003444111
NM_006060.6(IKZF1):c.247C>T (p.Arg83Ter) SNV
Germline/somatic		 Chr7:50376619 Pathogenic Condition: not provided
Acute lymphoid leukemia		 Criteria Provided
Multiple Submitters
No Conflicts
 rs_2153469119

2 SubmittersRCV001837716RCV003444112
NM_006060.6(IKZF1):c.161-8275C>T SNV
Germline		 Chr7:50368258 Conflicting classifications of pathogenicity Acute lymphoid leukemia
Condition: not provided
IKZF1-related disorder		 Criteria Provided
Conflicting Classifications

3 SubmittersRCV003325271RCV003883979RCV004753674
NM_016734.3(PAX5):c.77T>G (p.Val26Gly) SNV
Somatic		 Chr9:37020771 Likely pathogenic Acute lymphoid leukemia Criteria Provided
Single Submitter

1 SubmittersRCV003444115
NM_016734.3(PAX5):c.401C>G (p.Ser134Cys) SNV
Somatic		 Chr9:37015006 Likely pathogenic Acute lymphoid leukemia Criteria Provided
Single Submitter

1 SubmittersRCV003444116
NM_016734.3(PAX5):c.613G>T (p.Glu205Ter) SNV
Somatic		 Chr9:36966716 Likely pathogenic Acute lymphoid leukemia Criteria Provided
Single Submitter

1 SubmittersRCV003444119
NM_006060.6(IKZF1):c.475A>T (p.Asn159Tyr) SNV
Somatic		 Chr7:50382593 Likely pathogenic Acute lymphoid leukemia Criteria Provided
Single Submitter

1 SubmittersRCV003444121
NM_006060.6(IKZF1):c.271A>T (p.Lys91Ter) SNV
Somatic		 Chr7:50376643 Likely pathogenic Acute lymphoid leukemia Criteria Provided
Single Submitter

1 SubmittersRCV003444122
NM_016734.3(PAX5):c.46+1G>A SNV
Somatic		 Chr9:37033985 Likely pathogenic Acute lymphoid leukemia Criteria Provided
Single Submitter

1 SubmittersRCV003444124
NM_006060.6(IKZF1):c.450C>A (p.Cys150Ter) SNV
Somatic		 Chr7:50382568 Likely pathogenic Acute lymphoid leukemia Criteria Provided
Single Submitter

1 SubmittersRCV003444125
NM_016734.3(PAX5):c.1073G>A (p.Trp358Ter) SNV
Somatic		 Chr9:36846869 Likely pathogenic Acute lymphoid leukemia Criteria Provided
Single Submitter

1 SubmittersRCV003444131
NM_016734.3(PAX5):c.388C>A (p.Pro130Thr) SNV
Somatic		 Chr9:37015019 Likely pathogenic Acute lymphoid leukemia Criteria Provided
Single Submitter

1 SubmittersRCV003444138
NM_016734.3(PAX5):c.967G>T (p.Gly323Ter) SNV
Somatic		 Chr9:36882049 Likely pathogenic Acute lymphoid leukemia Criteria Provided
Single Submitter

1 SubmittersRCV003444139