NM_032638.5:c.156C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7

The NM_032638.5(GATA2):c.156C>T(p.Leu52Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,272 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 (★★). Synonymous variant affecting the same amino acid position (i.e. L52L) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

GATA2
NM_032638.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0880

Publications

0 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), G2P, Genomics England PanelApp
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: Orphanet, Ambry Genetics
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

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

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

BP6

Variant 3-128486876-G-A is Benign according to our data. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128486876-G-A is described in CliVar as Likely_benign. Clinvar id is 1542699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.088 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATA2	NM_032638.5 link	c.156C>T	p.Leu52Leu	synonymous_variant	Exon 2 of 6	ENST00000341105.7	NP_116027.2	P23769-1
GATA2	NM_001145661.2 link	c.156C>T	p.Leu52Leu	synonymous_variant	Exon 3 of 7		NP_001139133.1	P23769-1
GATA2	NM_001145662.1 link	c.156C>T	p.Leu52Leu	synonymous_variant	Exon 2 of 6		NP_001139134.1	P23769-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATA2	ENST00000341105.7 link	c.156C>T	p.Leu52Leu	synonymous_variant	Exon 2 of 6	1	NM_032638.5	ENSP00000345681.2		P23769-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000409

AC:

AN:

244638

AF XY:

0.00000754

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000910

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

6.85e-7

AC:

AN:

1460272

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

726274

show subpopulations

African (AFR)

AF:

0.0000299

AC:

AN:

33460

American (AMR)

AF:

0.00

AC:

AN:

44584

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25954

East Asian (EAS)

AF:

0.00

AC:

AN:

39662

South Asian (SAS)

AF:

0.00

AC:

AN:

85770

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53246

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1111528

Other (OTH)

AF:

0.00

AC:

AN:

60302

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Inborn genetic diseases

Benign:1

Dec 01, 2024

Ambry Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

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

Benign:1

Nov 04, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

2.5

(source)

DANN

Benign

0.93

PhyloP100

0.088

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over