rs2860228

Positions:

• chr3-128490824-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GATA2	NM_032638.5	c.-46+2075G>A		intron_variant		ENST00000341105.7
GATA2-AS1	NR_125398.1	n.759+755C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GATA2	ENST00000341105.7	c.-46+2075G>A		intron_variant		1	NM_032638.5	P1
GATA2-AS1	ENST00000669945.1	n.293+755C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.440

Alfa AF: 0.434 Hom.: 19075

Bravo AF: 0.433

Asia WGS AF: 0.356 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.0
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

Other links and lift over

dbSNP: rs2860228; hg19: chr3-128209667;