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NM_032638.5(GATA2):c.1347C>A (p.Ser449=)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 20, 2020
Accession:
VCV000404084.5
Variation ID:
404084
Description:
single nucleotide variant
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NM_032638.5(GATA2):c.1347C>A (p.Ser449=)

Allele ID
393299
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3q21.3
Genomic location
3: 128481115 (GRCh38) GRCh38 UCSC
3: 128199958 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_295:g.17073C>A
LRG_295t2:c.1347C>A LRG_295p2:p.Ser449=
NC_000003.11:g.128199958G>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000003.12:128481114:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00003
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00023
Trans-Omics for Precision Medicine (TOPMed) 0.00007
1000 Genomes Project 0.00020
Links
ClinGen: CA2599794
dbSNP: rs150052821
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Oct 20, 2020 RCV000466788.7
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV001150745.1
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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 Supporting information
Uncertain significance
(Oct 20, 2020)
criteria provided, single submitter
Method: clinical testing
Dendritic cell, monocyte, B lymphocyte, and natural killer lymphocyte deficiency
Lymphedema, primary, with myelodysplasia
Allele origin: germline
Invitae
Accession: SCV000541513.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change affects codon 449 of the GATA2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid … (more)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Lymphedema, primary, with myelodysplasia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001311835.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)

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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs150052821...

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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 04, 2021