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NM_032638.5(GATA2):c.1143+8C>T

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
2 (Most recent: Jul 12, 2021)
Last evaluated:
Jul 6, 2021
Accession:
VCV000700890.4
Variation ID:
700890
Description:
single nucleotide variant
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NM_032638.5(GATA2):c.1143+8C>T

Allele ID
689728
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3q21.3
Genomic location
3: 128481811 (GRCh38) GRCh38 UCSC
3: 128200654 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_295:g.16377C>T
LRG_295t2:c.1143+8C>T
NC_000003.11:g.128200654G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000003.12:128481810:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
1000 Genomes Project 0.00040
The Genome Aggregation Database (gnomAD) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Exome Aggregation Consortium (ExAC) 0.00004
Links
dbSNP: rs555534597
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Nov 17, 2020 RCV000869238.3
Uncertain significance 1 criteria provided, single submitter Jul 6, 2021 RCV001541977.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GATA2 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
823 849

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Likely benign
(Nov 17, 2020)
criteria provided, single submitter
Method: clinical testing
Dendritic cell, monocyte, B lymphocyte, and natural killer lymphocyte deficiency
Lymphedema, primary, with myelodysplasia
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV001010650.3
Submitted: (Jan 07, 2021)
Uncertain significance
(Jul 06, 2021)
criteria provided, single submitter
Method: curation
GATA2 deficiency with susceptibility to MDS/AML
Lymphedema, primary, with myelodysplasia
(Autosomal dominant inheritance)
Affected status: yes
Allele origin: unknown
Molecular Pathology Research Laboratory,SA Pathology
Accession: SCV001760612.1
Submitted: (Jul 12, 2021)
Publications:
PubMed (1)
PubMed: 33715335
Comment:
No criteria satisfied
Number of individuals with the variant: 1
Clinical Features:
Myelodysplasia (yes) , Acute Myeloid Leukemia (yes) , Hematological abnormality (yes) , Immunodeficiency (yes) , Lymphedema (yes)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Gynecologic manifestations in Emberger syndrome. YĆ¼ksel H Turkish journal of obstetrics and gynecology 2021 PMID: 33715335

Text-mined citations for rs555534597...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Dec 09, 2021