Variant chr3-128480137-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_032638.5(GATA2):c.*882T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0513 in 233,262 control chromosomes in the GnomAD database, including 382 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.054 ( 281 hom., cov: 33)

Exomes 𝑓: 0.047 ( 101 hom. )

Consequence

GATA2
NM_032638.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.237

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 links:

GATA2 (HGNC:):

GATA2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 3-128480137-A-T is Benign according to our data. Variant chr3-128480137-A-T is described in ClinVar as [Benign]. Clinvar id is 343116.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
GATA2	NM_032638.5 linkuse as main transcript	c.*882T>A	3_prime_UTR_variant	6/6	ENST00000341105.7	NP_116027.2	P23769-1
GATA2	NM_001145661.2 linkuse as main transcript	c.*882T>A	3_prime_UTR_variant	7/7		NP_001139133.1	P23769-1
GATA2	NM_001145662.1 linkuse as main transcript	c.*882T>A	3_prime_UTR_variant	6/6		NP_001139134.1	P23769-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATA2	ENST00000341105 linkuse as main transcript	c.*882T>A		3_prime_UTR_variant	6/6	1	NM_032638.5	ENSP00000345681.2		P23769-1

Frequencies

GnomAD3 genomes

AF:

0.0538

AC:

8191

AN:

152222

Hom.:

279

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0626

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.0815

Gnomad ASJ

AF:

0.0384

Gnomad EAS

AF:

0.00961

Gnomad SAS

AF:

0.0786

Gnomad FIN

AF:

0.0283

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0491

Gnomad OTH

AF:

0.0511

GnomAD4 exome

AF:

0.0466

AC:

3768

AN:

80922

Hom.:

101

Cov.:

AF XY:

0.0452

AC XY:

1680

AN XY:

37190

show subpopulations

Gnomad4 AFR exome

AF:

0.0632

Gnomad4 AMR exome

AF:

0.103

Gnomad4 ASJ exome

AF:

0.0355

Gnomad4 EAS exome

AF:

0.00746

Gnomad4 SAS exome

AF:

0.0627

Gnomad4 FIN exome

AF:

0.0500

Gnomad4 NFE exome

AF:

0.0513

Gnomad4 OTH exome

AF:

0.0525

GnomAD4 genome

AF:

0.0538

AC:

8202

AN:

152340

Hom.:

281

Cov.:

AF XY:

0.0534

AC XY:

3978

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.0626

Gnomad4 AMR

AF:

0.0819

Gnomad4 ASJ

AF:

0.0384

Gnomad4 EAS

AF:

0.00963

Gnomad4 SAS

AF:

0.0779

Gnomad4 FIN

AF:

0.0283

Gnomad4 NFE

AF:

0.0492

Gnomad4 OTH

AF:

0.0515

Alfa

AF:

0.0482

Hom.:

Bravo

AF:

0.0568

Asia WGS

AF:

0.0450

AC:

156

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Deafness-lymphedema-leukemia syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

6.4

DANN

Benign

0.82

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over