NM_032638.5:c.1018-19C>T

Variant summary

Our verdict is Benign. Variant got -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

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:13

Conservation

PhyloP100: -0.0490
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id is 257561.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-128481963-G-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GATA2NM_032638.5 linkc.1018-19C>T intron_variant Intron 4 of 5 ENST00000341105.7 NP_116027.2 P23769-1
GATA2NM_001145661.2 linkc.1018-19C>T intron_variant Intron 5 of 6 NP_001139133.1 P23769-1
GATA2NM_001145662.1 linkc.1018-61C>T intron_variant Intron 4 of 5 NP_001139134.1 P23769-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GATA2ENST00000341105.7 linkc.1018-19C>T intron_variant Intron 4 of 5 1 NM_032638.5 ENSP00000345681.2 P23769-1

Frequencies

GnomAD3 genomes
AF:
0.174
AC:
26426
AN:
151922
Hom.:
2467
Cov.:
33
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
GnomAD3 exomes
AF:
0.156
AC:
38589
AN:
246728
Hom.:
3336
AF XY:
0.156
AC XY:
20902
AN XY:
134120
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 SAS exome
AF:
0.0827
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.:
34
AF XY:
0.177
AC XY:
128671
AN XY:
726092
show subpopulations
Gnomad4 AFR exome
AF:
0.176
Gnomad4 AMR exome
AF:
0.124
Gnomad4 ASJ exome
AF:
0.128
Gnomad4 EAS exome
AF:
0.0518
Gnomad4 SAS exome
AF:
0.0851
Gnomad4 FIN exome
AF:
0.191
Gnomad4 NFE exome
AF:
0.196
Gnomad4 OTH exome
AF:
0.174
GnomAD4 genome
AF:
0.174
AC:
26441
AN:
152040
Hom.:
2468
Cov.:
33
AF XY:
0.171
AC XY:
12692
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.173
Gnomad4 AMR
AF:
0.155
Gnomad4 ASJ
AF:
0.117
Gnomad4 EAS
AF:
0.0534
Gnomad4 SAS
AF:
0.0731
Gnomad4 FIN
AF:
0.195
Gnomad4 NFE
AF:
0.194
Gnomad4 OTH
AF:
0.176
Alfa
AF:
0.178
Hom.:
1038
Bravo
AF:
0.173
Asia WGS
AF:
0.0710
AC:
247
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:13
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:7
Oct 31, 2016
Eurofins Ntd Llc (ga)
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Apr 03, 2018
PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

-
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

-
Clinical Genetics, Academic Medical Center
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

-
Genome Diagnostics Laboratory, University Medical Center Utrecht
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Nov 12, 2023
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 24% of patients studied by a panel of primary immunodeficiencies. Number of patients: 23. Only high quality variants are reported. -

not provided Benign:3
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Sep 14, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Nov 27, 2024
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Monocytopenia with susceptibility to infections Benign:1
Aug 10, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Deafness-lymphedema-leukemia syndrome;C3280030:Monocytopenia with susceptibility to infections Benign:1
Feb 04, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Deafness-lymphedema-leukemia syndrome Benign:1
Aug 10, 2021
Genome-Nilou Lab
Significance: 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
7.9
DANN
Benign
0.92
RBP_binding_hub_radar
1.1
RBP_regulation_power_radar
2.1

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.

Other links and lift over

dbSNP: rs11708606; hg19: chr3-128200806; COSMIC: COSV62004676; COSMIC: COSV62004676; API