rs1060503833
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001145661.2(GATA2):c.1386C>T(p.Ser462Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,454,652 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
GATA2
NM_001145661.2 synonymous
NM_001145661.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0810
Publications
0 publications found
Genes affected
GATA2 (HGNC:4171): (GATA binding protein 2) This gene encodes a member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes. The encoded protein plays an essential role in regulating transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Mar 2009]
GATA2 Gene-Disease associations (from GenCC):
- deafness-lymphedema-leukemia syndromeInheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp
- GATA2 deficiency with susceptibility to MDS/AMLInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- monocytopenia with susceptibility to infectionsInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics
- acute myeloid leukemiaInheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
- myelodysplastic syndromeInheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant 3-128481076-G-A is Benign according to our data. Variant chr3-128481076-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 412761.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.081 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001145661.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GATA2 | NM_001145661.2 | MANE Plus Clinical | c.1386C>T | p.Ser462Ser | synonymous | Exon 7 of 7 | NP_001139133.1 | ||
| GATA2 | NM_032638.5 | MANE Select | c.1386C>T | p.Ser462Ser | synonymous | Exon 6 of 6 | NP_116027.2 | ||
| GATA2 | NM_001145662.1 | c.1344C>T | p.Ser448Ser | synonymous | Exon 6 of 6 | NP_001139134.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GATA2 | ENST00000341105.7 | TSL:1 MANE Select | c.1386C>T | p.Ser462Ser | synonymous | Exon 6 of 6 | ENSP00000345681.2 | ||
| GATA2 | ENST00000487848.6 | TSL:1 MANE Plus Clinical | c.1386C>T | p.Ser462Ser | synonymous | Exon 7 of 7 | ENSP00000417074.1 | ||
| GATA2 | ENST00000430265.6 | TSL:1 | c.1344C>T | p.Ser448Ser | synonymous | Exon 6 of 6 | ENSP00000400259.2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1454652Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 722320 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1454652
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
722320
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33390
American (AMR)
AF:
AC:
0
AN:
44542
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25738
East Asian (EAS)
AF:
AC:
0
AN:
39546
South Asian (SAS)
AF:
AC:
0
AN:
85498
European-Finnish (FIN)
AF:
AC:
0
AN:
53072
Middle Eastern (MID)
AF:
AC:
0
AN:
5712
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1107116
Other (OTH)
AF:
AC:
0
AN:
60038
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
Deafness-lymphedema-leukemia syndrome;C3280030:Monocytopenia with susceptibility to infections (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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