rs2860228

Variant names:

• chr3-128490824-C-T
• rs2860228
• NM_032638.5:c.-46+2075G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032638.5(GATA2):​c.-46+2075G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,062 control chromosomes in the GnomAD database, including 14,092 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (14092 hom., cov: 32)
• Consequence: GATA2 NM_032638.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413
• Publications: 9 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-AS1 (HGNC:51108): (GATA2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATA2	NM_032638.5	MANE Select	c.-46+2075G>A		intron	N/A	NP_116027.2
	GATA2-AS1	NR_125398.1		n.759+755C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATA2	ENST00000341105.7	TSL:1 MANE Select	c.-46+2075G>A		intron	N/A	ENSP00000345681.2	P23769-1
	GATA2	ENST00000696466.1		c.26+1180G>A		intron	N/A	ENSP00000512647.1	A0A8Q3WLD0
	GATA2	ENST00000906584.1		c.-46+961G>A		intron	N/A	ENSP00000576643.1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64635 AN: 151944 Hom.: 14081 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.443

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.425 AC: 64689 AN: 152062 Hom.: 14092 Cov.: 32 AF XY: 0.420 AC XY: 31198 AN XY: 74338

African (AFR) AF: 0.467 AC: 19351 AN: 41452

American (AMR) AF: 0.440 AC: 6718 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1565 AN: 3468

East Asian (EAS) AF: 0.240 AC: 1241 AN: 5174

South Asian (SAS) AF: 0.438 AC: 2114 AN: 4822

European-Finnish (FIN) AF: 0.340 AC: 3594 AN: 10578

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28576 AN: 67970

Other (OTH) AF: 0.440 AC: 929 AN: 2110

Alfa AF: 0.429 Hom.: 41471

Bravo AF: 0.433

Asia WGS AF: 0.356 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.0
DANN	Benign	0.82
PhyloP100		0.41
PromoterAI		0.0072	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2860228; hg19: chr3-128209667;