About GATA2
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
GATA2 c.710G>A, p.(Gly237Asp)
Classification
Benign
Variant description:
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is benign. Select a step to read what it means.
Benign.A benign classification under the recorded framework.
In plain language
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.
LYFE Sciences is an AI system, and it can make mistakes.
Criteria may be applied incorrectly, sources may be misread, and a
confident-looking classification can still be wrong.
Double-check every criterion and its underlying evidence
before relying on any call.
01The reasoning
How it was classified
The recorded framework is Not recorded. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
Recorded applied criteria
The applied criteria and their strengths are shown as assessed under the stated framework.
Pathogenic evidence criteria: 0
Benign evidence criteria: 4
Pathogenic criteria applied · 0
No pathogenic criterion marked as applied in the recorded assessment.
Benign criteria applied · 4
BS1Strong
BS1 · strong
The variant has a total allele frequency of 0.366% (1033/282138 alleles) in gnomAD v2.1, which exceeds the 0.3% BS1 threshold. This frequency is greater than expected for GATA2 deficiency, a rare dominant disorder.
BS2Strong
BS2 · strong
Seventeen homozygotes are observed in gnomAD v2.1 (37 in gnomAD v4.1). GATA2 deficiency is a dominant disorder with high penetrance; the presence of homozygous individuals in a population database is incompatible with a pathogenic variant in this gene.
BP4Supporting
BP4 · supporting
Multiple computational predictors suggest no impact: SpliceAI max delta 0.00 (no predicted splice alteration), REVEL score 0.401 (below 0.5 threshold for predicted damaging), and BayesDel score -0.00217913 (in the benign range).
BP6Supporting
BP6 · supporting
Eight clinical laboratory submissions in ClinVar (ID 343139) classify this variant as Likely benign (4 laboratories) or Benign (4 laboratories). Although review status is 'criteria provided, single submitter' per submission, the consensus across multiple independent clinical laboratories supports a benign interpretation.
Recorded classification: Benign
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BS1 strong benign, BS2 strong benign, BP4 supporting benign, BP6 supporting benign; combination = 2 strong benign + 2 supporting benign, which maps to Benign.
02The sources
Evidence at a glance
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1
gnomAD v2.1
Population frequency
2,489 / 1,614,026 alleles
gnomAD v4.1: 2,489 / 1,614,026 alleles. Recorded AF 0.00154211. Recorded homozygote count 37.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0.00366133; MAF= 0.36613%, 1033/282138 alleles, homozygotes = 17) and has highest observed frequency in the European (Finnish) population (AF= 0.0376117; MAF= 3.76117%, 943/25072 alleles, homozygotes = 17); grpmax FAF= 0.00065149.
gnomAD-Canada
This variant is present in gnomAD-Canada v1.0 (AF= 0.00021734405564007825, 4/18404 alleles, homozygotes = 0).
SpliceAI score
0.000 maximum delta
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
ClinVar submissions
8 reported laboratory submissions
4 Likely benign · 4 Benign. ClinVar API review status: criteria provided, multiple submitters, no conflicts.
Functional evidence
Statement recorded
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. GATA2, a transcription factor, is recurrently mutated in hematological malignancies and various solid tumors.
No listed criterion applied
OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
No matching record reported
This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.
Context only
For specialists
Technical detail
ACMG/AMP criteria under Not recorded, with the data and sources behind each one.
29 criteria with recorded statuses: 4 met · 12 not met · 7 not assessed · 6 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
NM_001145661.1:c.710G>A (p.Gly237Asp) in GATA2 is classified as Benign based on generic ACMG/AMP 2015 criteria.
This variant is present in gnomAD v2.1 at an allele frequency of 0.366% (1033/282138 alleles, including 17 homozygotes), exceeding the BS1 threshold of 0.3% for a rare dominant disorder.
Seventeen homozygous individuals are observed in gnomAD v2.1 (37 in gnomAD v4.1). Homozygosity for a variant in a gene causing a highly penetrant dominant disorder (GATA2 deficiency) is strong evidence of a benign effect (BS2).
Multiple in silico predictors support a benign interpretation: SpliceAI predicts no splice impact (max delta 0.00), REVEL score is 0.401 (below 0.5 threshold), and BayesDel score is -0.00217913 (benign range) (BP4).
Eight clinical laboratories in ClinVar classify this variant as Likely benign (4) or Benign (4), consistent with a benign interpretation (BP6).
No criteria match.
Met · 4
BS1 StrongThe variant has a total allele frequency of 0.366% (1033/282138 alleles) in gnomAD v2.1, which exceeds the 0.3% BS1 threshold. This frequency is greater than expected for GATA2 deficiency, a rare dominant disorder. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1 total AF 0.366% (> 0.3% BS1 threshold)
- 1033 alleles
- 17 homozygotes
- gnomAD v4.1 total AF 0.154%.
Sources
BS2 StrongSeventeen homozygotes are observed in gnomAD v2.1 (37 in gnomAD v4.1). GATA2 deficiency is a dominant disorder with high penetrance; the presence of homozygous individuals in a population database is incompatible with a pathogenic variant in this gene. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1: 17 homozygotes
- gnomAD v4.1: 37 homozygotes. Homozygosity for a dominant disease gene is strong evidence of benign impact.
Still missing
- gnomAD does not provide phenotype confirmation of healthy status
- but homozygous observation in a population database is incompatible with a dominant Mendelian disorder.
Sources
BP4 SupportingMultiple computational predictors suggest no impact: SpliceAI max delta 0.00 (no predicted splice alteration), REVEL score 0.401 (below 0.5 threshold for predicted damaging), and BayesDel score -0.00217913 (in the benign range). Details ▾Hide ▴
Evidence considered
- SpliceAI max delta 0.00
- REVEL 0.401
- BayesDel -0.00217913 (benign). All three in silico predictors are consistent with a benign variant.
Sources
BP6 SupportingEight clinical laboratory submissions in ClinVar (ID 343139) classify this variant as Likely benign (4 laboratories) or Benign (4 laboratories). Although review status is 'criteria provided, single submitter' per submission, the consensus across multiple independent clinical laboratories supports a benign interpretation. Details ▾Hide ▴
Evidence considered
- ClinVar ID 343139: 4 laboratories report Likely benign
- 4 report Benign. Submitters include Invitae
- Ambry Genetics
- PreventionGenetics
- Fulgent Genetics
- and others.
Still missing
- No expert panel review available for this ClinVar entry.
Sources
Not met · 12 · evaluated, threshold not reached
PS1 No evidence of a different nucleotide change at the same amino acid residue (Gly237) resulting in a known pathogenic variant. No same-residue comparator variants were identified. Details ▾Hide ▴
Evidence considered
- PM5 candidate harvesting found no same-residue comparator variants for position 237.
Still missing
- No ClinVar entries for alternative nucleotide changes at Gly237 were identified.
Sources
pm5_candidates
PS3 No variant-specific functional studies were identified. OncoKB reports unknown oncogenic effect with no curated functional evidence for this specific variant. No publications with functional data for NM_001145661.1:c.710G>A were found. Details ▾Hide ▴
Evidence considered
- OncoKB reports 'Unknown Oncogenic Effect' for GATA2 G237D with no variant-specific functional evidence.
Still missing
- No in vitro or in vivo functional studies available for this variant.
Sources
PS4 The variant is present at 0.366% total allele frequency in gnomAD v2.1, which is inconsistent with a rare pathogenic variant. No case-control studies demonstrating enrichment in affected individuals were identified. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1: 1033/282138 alleles (0.366%)
- gnomAD v4.1: 2489/1614026 alleles (0.154%).
Still missing
- No case-control or cohort enrichment data available.
Sources
PM1 The variant does not lie in a statistically significant mutational hotspot per cancerhotspots.org. Additionally, the high population frequency in the Finnish population (3.76% AF, 17 homozygotes) is inconsistent with a critical functional domain intolerant to benign variation. Details ▾Hide ▴
Evidence considered
- Not in a statistically significant hotspot
- Finnish AF 3.76% with 17 homozygotes argues against location in a critical functional domain.
Sources
PM2 Variant is present in gnomAD v2.1 at total allele frequency 0.366% (1033/282138 alleles), exceeding the 0.1% PM2 threshold for rarity. This variant is not absent from population databases. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1 total AF 0.366% (> 0.1% PM2 threshold)
- gnomAD v4.1 total AF 0.154%.
Sources
PP2 Although GATA2 missense variants are a known disease mechanism in GATA2 deficiency syndrome, this specific variant is present at high population frequency (3.76% in Finnish, 17 homozygotes), which is incompatible with a pathogenic missense variant in a dominant disorder gene. Details ▾Hide ▴
Evidence considered
- Finnish AF 3.76% with 17 homozygotes is inconsistent with a pathogenic missense in a gene where missense is a disease mechanism.
Sources
PP3 Multiple in silico predictors suggest no damaging effect: REVEL score 0.401 (below 0.5 threshold), BayesDel score -0.00217913 (benign range), SpliceAI max delta 0.00 (no predicted splice impact). No computational evidence supports a deleterious effect. Details ▾Hide ▴
Evidence considered
- REVEL 0.401 (<0.5)
- BayesDel -0.00217913 (benign)
- SpliceAI max delta 0.00 (no splice effect).
Sources
PP5 ClinVar reports this variant as Likely benign (4 clinical laboratories) and Benign (4 clinical laboratories). No reputable source reports it as pathogenic. The ClinVar-associated PMIDs (25741868, 32171751, 20963938, 33226740) do not mention this variant. Details ▾Hide ▴
Evidence considered
- ClinVar ID 343139: 8 clinical laboratories classify as Likely benign or Benign
- no submitter reports pathogenic.
Sources
BA1 Total allele frequency in gnomAD v2.1 is 0.366%, below the 1% BA1 threshold. Although the Finnish subpopulation AF is 3.76%, BA1 uses the overall population frequency. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1 total AF 0.366% (< 1% BA1 threshold)
- Finnish subpopulation AF 3.76% does not independently trigger BA1.
Sources
BS3 No variant-specific well-established functional studies demonstrating no damaging effect were identified. In silico evidence is addressed under BP4. Details ▾Hide ▴
Evidence considered
- No functional studies available for this variant
- OncoKB reports no variant-specific functional evidence.
Still missing
- No in vitro functional studies demonstrating normal GATA2 function for this variant.
BP1 GATA2 deficiency is caused by both missense and truncating variants. Missense is a recognized pathogenic mechanism in this gene; BP1 is only applicable when a gene's disease mechanism is exclusively through truncating variants. Details ▾Hide ▴
Evidence considered
- GATA2 deficiency is caused by both missense and loss-of-function variants per published literature (PMID:40821825
- PMID:33759087
- PMID:39885120).
Sources
pvs1_gene_context
PS5 No reputable source reports this variant as pathogenic. ClinVar classification is Likely benign (4 laboratories) and Benign (4 laboratories). None of the associated PMIDs mention this specific variant. Details ▾Hide ▴
Evidence considered
- ClinVar ID 343139: 4 laboratories report Likely benign
- 4 report Benign
- no submitter reports pathogenic.
Sources
Not assessed · 7 · no assessment recorded
PS2 No de novo data available for this variant. No publications or ClinVar submissions report de novo occurrence. Details ▾Hide ▴
Still missing
- No parental testing or de novo reports available.
PM6 No de novo data available for this variant. No publications or ClinVar submissions report de novo occurrence. Details ▾Hide ▴
Still missing
- No parental testing or de novo reports available.
PP1 No co-segregation data available for this variant. Details ▾Hide ▴
Still missing
- No family studies or segregation analysis available.
PP4 No patient phenotype information available to assess phenotypic specificity. Details ▾Hide ▴
Still missing
- No phenotype data for affected individuals carrying this variant.
BS4 No segregation data available to assess lack of co-segregation with disease. Details ▾Hide ▴
Still missing
- No family segregation data available.
BP2 No data on whether this variant has been observed in trans with a known pathogenic GATA2 variant. Details ▾Hide ▴
Still missing
- No phasing data available.
BP5 No information on whether this variant has been observed in cases with an alternate molecular basis for disease. Details ▾Hide ▴
Still missing
- No data on alternate causal variants in individuals carrying this variant.
Not applicable · 6· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/AMissense substitution (c.710G>A, p.Gly237Asp) does not fall into null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus. PVS1 is not applicable to missense variants. Details ▾Hide ▴
Evidence considered
- NM_001145661.1:c.710G>A is a missense variant in exon 4
- classified as 'other' by the generic PVS1 decision framework.
Sources
pvs1_generic_framework ↗pvs1_variant_assessment
PM3 N/AGATA2 deficiency is an autosomal dominant disorder; PM3 (detection in trans with a pathogenic variant) is applicable only to recessive disorders. Details ▾Hide ▴
No further detail was recorded.
PM4 N/AThis is a substitution variant, not a nonstop or in-frame insertion/deletion. PM4 applies only to protein length-altering variants. Details ▾Hide ▴
No further detail was recorded.
PM5 N/AUnable to confirm classic same-residue PM5 semantics; no comparator pathogenic missense variants at Gly237 were identified in candidate harvesting. Details ▾Hide ▴
Evidence considered
- PM5 candidate harvesting returned 0 candidates
- same-residue pathogenic comparator not available.
Sources
pm5_candidates
BP3 N/AThis is a substitution variant, not an in-frame deletion/insertion in a repetitive region. Details ▾Hide ▴
No further detail was recorded.
BP7 N/AThis is a missense variant (c.710G>A, p.Gly237Asp), not a synonymous variant. BP7 applies only to synonymous variants with no predicted splice effect. Details ▾Hide ▴
No further detail was recorded.
Identifiers
- Gene
- GATA2
- Transcript
- NM_001145661.1
- Coding (HGVS c.)
- NM_001145661.1:c.710G>A
- Protein (HGVS p.)
- NP_001139133.1:p.(Gly237Asp)
- GRCh38
- chr3:128485888 C>T
- GRCh37
- chr3:128204731 C>T
- ClinVar
- 343139
Gene diagram
Every interpreted variant in GATA2, mapped onto the exon structure of NM_001145661.1. Select a row to find it on the plot.
GATA2NM_001145661.1
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in GATA2
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Select a row to find it on the plot; use the link to open its page.
| Protein | Location | Classification | Link |
|---|
gnomAD v4.1
2,489 / 1,614,026 alleles
AF 0.00154 · 37 homozygotes · FAF 0.00019
gnomAD v2.1
1,033 / 282,138 alleles
AF 0.00366 · 17 homozygotes · FAF 0.000651
gnomAD-Canada v1.0
Allele count data not recorded
By genetic ancestry
gnomAD v4.1
AF 0.0015 · 2489 / 1,614,026 alleles · 37 hom · FAF 0.00019
| European (Finnish)2185 / 64,028 | 0.03437 hom |
| Remaining individuals46 / 62,496 | 0.00074 |
| European (non-Finnish)250 / 1,179,952 | 0.00021 |
| Admixed American6 / 60,010 | 0.0001 |
| East Asian1 / 44,880 | 2.2e-05 |
| South Asian1 / 91,070 | 1.1e-05 |
0 alternate alleles recorded in 4 other groups: Amish, Middle Eastern, Ashkenazi Jewish, African/African American.
gnomAD v2.1
AF 0.0037 · 1033 / 282,138 alleles · 17 hom · FAF 0.00065
| European (Finnish)943 / 25,072 | 0.03817 hom |
| Remaining individuals17 / 7,202 | 0.0024 |
| European (non-Finnish)68 / 128,630 | 0.00053 |
| Admixed American5 / 35,416 | 0.00014 |
0 alternate alleles recorded in 4 other groups: African/African American, Ashkenazi Jewish, East Asian, South Asian.
gnomAD-Canada
AF not recorded · ? / ? alleles
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 0.00154211; MAF= 0.15421%, 2489/1614026 alleles, homozygotes = 37) and has highest observed frequency in the European (Finnish) population (AF= 0.0341257; MAF= 3.41257%, 2185/64028 alleles, homozygotes = 37); grpmax FAF= 0.00019008.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0.00366133; MAF= 0.36613%, 1033/282138 alleles, homozygotes = 17) and has highest observed frequency in the European (Finnish) population (AF= 0.0376117; MAF= 3.76117%, 943/25072 alleles, homozygotes = 17); grpmax FAF= 0.00065149.
gnomAD-Canada
This variant is present in gnomAD-Canada v1.0 (AF= 0.00021734405564007825, 4/18404 alleles, homozygotes = 0).
SpliceAI and Pangolin
Other predictors
- REVEL
- 0.401
- BayesDel
- -0.002
How the predictions were used
BP4 SupportingMultiple computational predictors suggest no impact: SpliceAI max delta 0.00 (no predicted splice alteration), REVEL score 0.401 (below 0.5 threshold for predicted damaging), and BayesDel score -0.00217913 (in the benign range). Details ▾Hide ▴
Evidence considered
- SpliceAI max delta 0.00
- REVEL 0.401
- BayesDel -0.00217913 (benign). All three in silico predictors are consistent with a benign variant.
Sources
PP3 Multiple in silico predictors suggest no damaging effect: REVEL score 0.401 (below 0.5 threshold), BayesDel score -0.00217913 (benign range), SpliceAI max delta 0.00 (no predicted splice impact). No computational evidence supports a deleterious effect. Details ▾Hide ▴
Evidence considered
- REVEL 0.401 (<0.5)
- BayesDel -0.00217913 (benign)
- SpliceAI max delta 0.00 (no splice effect).
Sources
BP7 N/AThis is a missense variant (c.710G>A, p.Gly237Asp), not a synonymous variant. BP7 applies only to synonymous variants with no predicted splice effect. Details ▾Hide ▴
No further detail was recorded.
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.401. BayesDel score = -0.00217913.
7 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
Recorded publications
-
PMID 25741868 ↗Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.Standards and guidelines for the interpretation of sequence variants (ACMG/AMP 2015). This is a methodological consensus paper that does not report on any specific GATA2 variant. NM_001145661.1:c.710G>A was not identified in this paper.Does not name this variant
-
PMID 20963938 ↗CEBPA-Associated Familial Acute Myeloid Leukemia (AML).Adam MP et al. · 1993GeneReviews chapter on CEBPA-Associated Familial Acute Myeloid Leukemia. This paper discusses the CEBPA gene, not GATA2. NM_001145661.1:c.710G>A was not identified in this paper.Does not name this variant
-
PMID 32171751 ↗Acute myeloid leukaemia in adult patients: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up.Heuser M et al. · 2020ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up of acute myeloid leukaemia in adult patients. This is a general clinical guideline that mentions germline predisposition to myeloid neoplasms at the gene level but does not discuss any specific GATA2 variant. NM_001145661.1:c.710G>A was not identified in this paper.Does not name this variant
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PMID 33226740 ↗ETV6-Related Thrombocytopenia and Predisposition to Leukemia.Adam MP et al. · 1993GeneReviews chapter on ETV6-Related Thrombocytopenia and Predisposition to Leukemia. This paper discusses the ETV6 gene, not GATA2. NM_001145661.1:c.710G>A was not identified in this paper.Does not name this variant
-
PMID 23037933 ↗Including the initial newborn screening bloodspot collection device serial number on birth certificates: basis and recommendations from the Secretary of Health and Human Services' Advisory Committee on Heritable Disorders in Newborns and Children.Therrell BL et al. · 2013Recommendations on newborn screening bloodspot collection device serial numbers. This paper is unrelated to GATA2 or variant interpretation. NM_001145661.1:c.710G>A was not identified in this paper.Does not name this variant
-
PMID 24394680 ↗Parental permission for pilot newborn screening research: guidelines from the NBSTRN.Guidelines for parental permission in pilot newborn screening research. This paper is unrelated to GATA2 or variant interpretation. NM_001145661.1:c.710G>A was not identified in this paper.Does not name this variant
-
PMID 28492532 ↗Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. This is a methodological paper describing a variant classification framework, not a report on any specific GATA2 variant. NM_001145661.1:c.710G>A was not identified in this paper.Does not name this variant
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
2,489 / 1,614,026 recorded alleles
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.000
Open source ↗
ClinVar
4 Likely benign · 4 Benign
Open source ↗
COSMIC
Captured COSMIC source record
Open source ↗
Cancer hotspots
Captured Cancer Hotspots source record
Open source ↗
OncoKB
Captured OncoKB source record
Open source ↗
All source links
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/variation/343139/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/3-128204731-C-T?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr3-128485888-C-T?dataset=gn…
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/3-128485888-C-T
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_001145661.1%3Ac.7…
- OncoKB ↗www.oncokb.org/gene/GATA2/G237D
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=GATA2+c.710G%3EA
- Cancer hotspots ↗www.cancerhotspots.org/
Statements for reports
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 0.00154211; MAF= 0.15421%, 2489/1614026 alleles, homozygotes = 37) and has highest observed frequency in the European (Finnish) population (AF= 0.0341257; MAF= 3.41257%, 2185/64028 alleles, homozygotes = 37); grpmax FAF= 0.00019008.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0.00366133; MAF= 0.36613%, 1033/282138 alleles, homozygotes = 17) and has highest observed frequency in the European (Finnish) population (AF= 0.0376117; MAF= 3.76117%, 943/25072 alleles, homozygotes = 17); grpmax FAF= 0.00065149.
gnomAD-Canada
This variant is present in gnomAD-Canada v1.0 (AF= 0.00021734405564007825, 4/18404 alleles, homozygotes = 0).
ClinVar
This variant has been reported in ClinVar as Likely benign (4 clinical laboratories) and as Benign (4 clinical laboratories). (ClinVarID = 343139)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.401. BayesDel score = -0.00217913.
Functional
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. GATA2, a transcription factor, is recurrently mutated in hematological malignancies and various solid tumors.
Somatic
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.