Back
NM_001145661.1:c.856G>C
p.Ala286Pro · GATA2
ACMG/AMP
0%
complete
Final classification
VUS
PM2
GATA2
c.856G>C
p.Ala286Pro
This variant

The GATA2 c.856G>C (p.Ala286Pro) variant has been reported in ClinVar as a variant of uncertain significance with three clinical laboratory submissions.

Transcript
NM_001145661.1
HGVS · transcript:coding
NM_001145661.1:c.856G>C
GRCh38
chr3:128485742 C>G
GRCh37
chr3:128204585 C>G
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
GATA2 c.856G>C

The GATA2 c.856G>C (p.Ala286Pro) variant has been reported in ClinVar as a variant of uncertain significance with three clinical laboratory submissions.1 This variant is absent from gnomAD v2.1 and is present only once in gnomAD v4.1 (AF 6.19681e-07; 1/1613734 alleles), which supports rarity in population databases.2 Computational evidence does not strongly support either a damaging or benign effect: SpliceAI predicts no significant splice impact (max delta score 0.00), REVEL is 0.352, and BayesDel is -0.0703764.3

PM2 VUS
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.
Gene diagram · NM_001145661.1 · variants mapped to exon structure
GATA2 NM_001145661.1
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 21 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting review Pathogenic
This variant is absent from gnomAD v2.1 and present only once in gnomAD v4.1 (AF 6.19681e-07; 1/1613734 alleles; highest subpopulation AF 8.47469e-07), which is far below the 0.1% rarity threshold and supports rarity in population databases.
Absent from gnomAD v2.1.Present once in gnomAD v4.1 at extremely low frequency.
Assessed · not applied · 5 not met · 16 not assessed
Pathogenic
PS1 No alternate nucleotide change producing the same p.Ala286Pro amino acid substitution was identified from the available evidence, so PS1 was not applied.
PS2 No confirmed de novo occurrence with parental relationship confirmation was identified for this variant, so PS2 was not applied.
PS3 No well-established functional study showing a damaging effect for p.Ala286Pro was identified in the available evidence, so PS3 was not applied.
PS4 The available evidence does not provide a case-control enrichment analysis or sufficient independent affected-case count for this variant, so PS4 was not applied.
PM1 Available hotspot review did not identify codon 286 as a statistically significant hotspot, so there is insufficient evidence that this variant lies in a well-established critical region without benign variation.
PM6 No assumed de novo occurrence without full parental confirmation was identified for this variant, so PM6 was not applied.
PP1 No segregation data were identified for this variant, so PP1 was not applied.
PP2 Available evidence does not establish a gene-level missense-specific constraint or a validated missense-prone mechanism at this residue sufficient to apply PP2.
PP3 Computational evidence is not strong enough to support a damaging prediction.
PP4 No patient phenotype, laboratory phenotype, or disease-specific clinical presentation data were provided for this variant, so PP4 was not applied.
PP5 Although this variant is present in ClinVar, the available record does not provide an independent reputable-source assertion that can be used here for PP5.
Benign
BA1 The observed population frequency is far below the 1% benign stand-alone threshold.
BS1 The observed population frequency is far below the 0.3% threshold typically used for BS1.
BS2 No evidence was identified showing this variant in well-phenotyped healthy adult individuals at a level sufficient for BS2.
BS3 No well-established functional study showing normal protein function for p.Ala286Pro was identified, so BS3 was not applied.
BS4 No non-segregation data were identified for this variant, so BS4 was not applied.
BP1 Available evidence is insufficient to conclude that missense variation in GATA2 is consistently less likely to be disease-causing than truncating variation, so BP1 was not applied.
BP2 No phase data or second-variant data were identified for this case, so BP2 was not applied.
BP4 Computational evidence does not provide sufficiently strong benign support.
BP5 No alternate molecular diagnosis or independent cause for the phenotype was provided, so BP5 was not applied.
BP6 The available evidence does not provide an independent reputable-source benign classification that can be used here for BP6.
N/A · 6 PVS1 · PM3 · PM4 · PM5 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 6.19681e-07; MAF= 0.00006%, 1/1613734 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47469e-07; MAF= 0.00008%, 1/1179984 alleles, homozygotes = 0).
v2.1
Absent from gnomAD v2.1.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
6.2e-05% · 1 / 1,613,734
0 hom
European (non-Finnish)
1 / 1,179,984
8.5e-05%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories). (ClinVarID = 934804)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.352. BayesDel score = -0.0703764.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
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.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
7Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 12 PMIDs not cited in assessment
23619275 ↗ ACMG position statement on prenatal/preconception expanded carrier screening. CLINVAR
23652378 ↗ A framework to start the debate on neonatal screening policies in the EU: an Expert Opinion Document. CLINVAR
25626707 ↗ Whole-genome sequencing in newborn screening? A statement on the continued importance of targeted approaches in newborn screening programmes. CLINVAR
25730230 ↗ Expanded carrier screening in reproductive medicine-points to consider: a joint statement of the American College of Medical Genetics and Genomics, American College of Obstetricians and Gynecologists, National Society of Genetic Counselors, Perinatal Quality Foundation, and Society for Maternal-Fetal Medicine. CLINVAR
23169492 ↗ The perspective from EASAC and FEAM on direct-to-consumer genetic testing for health-related purposes. CLINVAR
24121147 ↗ Appropriateness of newborn screening for α1-antitrypsin deficiency. CLINVAR
22947299 ↗ Specific guidelines for assessing and improving the methodological quality of economic evaluations of newborn screening. CLINVAR
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. CLINVAR
23881473 ↗ Newborn screening: education, consent, and the residual blood spot. The position of the national society of genetic counselors. CLINVAR
24022298 ↗ Offering prenatal diagnostic tests: European guidelines for clinical practice [corrected]. CLINVAR
24394680 ↗ Parental permission for pilot newborn screening research: guidelines from the NBSTRN. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR