rs11708606

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_032638.5(GATA2):c.1018-19C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 1,611,562 control chromosomes in the GnomAD database, including 27,415 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2468 hom., cov: 33)

Exomes 𝑓: 0.18 ( 24947 hom. )

Consequence

GATA2
NM_032638.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:14

Conservation

PhyloP100: -0.0490

Publications

11 publications found

Variant links:

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 syndrome
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, G2P
GATA2 deficiency with susceptibility to MDS/AML
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
monocytopenia with susceptibility to infections
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet
acute myeloid leukemia
Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
myelodysplastic syndrome
Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp

GATA2 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_032638.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 3-128481963-G-A is Benign according to our data. Variant chr3-128481963-G-A is described in ClinVar as Benign. ClinVar VariationId is 257561.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032638.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GATA2	NM_001145661.2	MANE Plus Clinical	c.1018-19C>T	intron	N/A	NP_001139133.1	P23769-1
GATA2	NM_032638.5	MANE Select	c.1018-19C>T	intron	N/A	NP_116027.2
GATA2	NM_001145662.1		c.1018-61C>T	intron	N/A	NP_001139134.1	P23769-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GATA2	ENST00000341105.7	TSL:1 MANE Select	c.1018-19C>T	intron	N/A	ENSP00000345681.2	P23769-1
GATA2	ENST00000487848.6	TSL:1 MANE Plus Clinical	c.1018-19C>T	intron	N/A	ENSP00000417074.1	P23769-1
GATA2	ENST00000430265.6	TSL:1	c.1018-61C>T	intron	N/A	ENSP00000400259.2	P23769-2

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26426

AN:

151922

Hom.:

2467

Cov.:

show subpopulations

Gnomad AFR

AF:

0.173

Gnomad AMI

AF:

0.205

Gnomad AMR

AF:

0.155

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.0534

Gnomad SAS

AF:

0.0722

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.172

Gnomad NFE

AF:

0.194

Gnomad OTH

AF:

0.178

GnomAD2 exomes

AF:

0.156

AC:

38589

AN:

246728

AF XY:

0.156

show subpopulations

Gnomad AFR exome

AF:

0.174

Gnomad AMR exome

AF:

0.119

Gnomad ASJ exome

AF:

0.129

Gnomad EAS exome

AF:

0.0538

Gnomad FIN exome

AF:

0.191

Gnomad NFE exome

AF:

0.198

Gnomad OTH exome

AF:

0.175

GnomAD4 exome

AF:

0.181

AC:

263459

AN:

1459522

Hom.:

24947

Cov.:

AF XY:

0.177

AC XY:

128671

AN XY:

726092

show subpopulations

African (AFR)

AF:

0.176

AC:

5897

AN:

33472

American (AMR)

AF:

0.124

AC:

5536

AN:

44694

Ashkenazi Jewish (ASJ)

AF:

0.128

AC:

3338

AN:

26128

East Asian (EAS)

AF:

0.0518

AC:

2055

AN:

39690

South Asian (SAS)

AF:

0.0851

AC:

7342

AN:

86250

European-Finnish (FIN)

AF:

0.191

AC:

9803

AN:

51398

Middle Eastern (MID)

AF:

0.170

AC:

979

AN:

5768

European-Non Finnish (NFE)

AF:

0.196

AC:

218008

AN:

1111776

Other (OTH)

AF:

0.174

AC:

10501

AN:

60346

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

11113

22227

33340

44454

55567

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7526

15052

22578

30104

37630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.174

AC:

26441

AN:

152040

Hom.:

2468

Cov.:

AF XY:

0.171

AC XY:

12692

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.173

AC:

7157

AN:

41442

American (AMR)

AF:

0.155

AC:

2375

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.117

AC:

406

AN:

3468

East Asian (EAS)

AF:

0.0534

AC:

275

AN:

5152

South Asian (SAS)

AF:

0.0731

AC:

352

AN:

4816

European-Finnish (FIN)

AF:

0.195

AC:

2062

AN:

10588

Middle Eastern (MID)

AF:

0.178

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.194

AC:

13202

AN:

67964

Other (OTH)

AF:

0.176

AC:

373

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

1090

2180

3270

4360

5450

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

270

540

810

1080

1350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.178

Hom.:

2027

Bravo

AF:

0.173

Asia WGS

AF:

0.0710

AC:

247

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (8)

not provided (3)

Deafness-lymphedema-leukemia syndrome (1)

Deafness-lymphedema-leukemia syndrome;C3280030:Monocytopenia with susceptibility to infections (1)

Monocytopenia with susceptibility to infections (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

7.9

(source)

DANN

Benign

0.92

PhyloP100

-0.049

RBP_binding_hub_radar

1.1

RBP_regulation_power_radar

2.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over