rs1806462

Positions:

• chr3-128487775-C-A
• chr3-128487775-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145661.2(GATA2):​c.-110G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,068 control chromosomes in the GnomAD database, including 14,058 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 0.42 (14039 hom., cov: 32)
  • Exomes 𝑓: 0.39 (19 hom.)
• Consequence: GATA2 NM_001145661.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GATA2	NM_032638.5	c.-45-699G>T		intron_variant		ENST00000341105.7	NP_116027.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATA2	ENST00000341105.7	c.-45-699G>T		intron_variant		1	NM_032638.5	ENSP00000345681.2

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64443 AN: 151776 Hom.: 14028 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.444

GnomAD4 exome AF: 0.385 AC: 67 AN: 174 Hom.: 19 Cov.: 0 AF XY: 0.355 AC XY: 44 AN XY: 124

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 NFE exome AF: 0.373

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.425 AC: 64496 AN: 151894 Hom.: 14039 Cov.: 32 AF XY: 0.418 AC XY: 31056 AN XY: 74218

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.441

Alfa AF: 0.294 Hom.: 892

Bravo AF: 0.433

Asia WGS AF: 0.355 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	1.6
DANN	Benign	0.81
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3

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: rs1806462; hg19: chr3-128206618;