rs2335052

Positions:

• chr3-128486108-C-G
• chr3-128486108-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_032638.5(GATA2):​c.490G>C​(p.Ala164Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A164T) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: GATA2 NM_032638.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.15685388).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GATA2	NM_001145661.2	c.490G>C	p.Ala164Pro	missense_variant	4/7	ENST00000487848.6	NP_001139133.1
GATA2	NM_032638.5	c.490G>C	p.Ala164Pro	missense_variant	3/6	ENST00000341105.7	NP_116027.2
GATA2	NM_001145662.1	c.490G>C	p.Ala164Pro	missense_variant	3/6		NP_001139134.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATA2	ENST00000341105.7	c.490G>C	p.Ala164Pro	missense_variant	3/6	1	NM_032638.5	ENSP00000345681	P1
GATA2	ENST00000487848.6	c.490G>C	p.Ala164Pro	missense_variant	4/7	1	NM_001145661.2	ENSP00000417074	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 40

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Uncertain	0.083	D
BayesDel_noAF	Benign	-0.12
CADD	Benign	18
DANN	Uncertain	0.99
DEOGEN2	Benign	0.29	T;.;T
Eigen	Benign	-0.43
Eigen_PC	Benign	-0.32
FATHMM_MKL	Benign	0.67	D
LIST_S2	Benign	0.63	.;T;T
M_CAP	Uncertain	0.25	D
MetaRNN	Benign	0.16	T;T;T
MetaSVM	Uncertain	0.55	D
MutationAssessor	Benign	0.34	N;N;N
MutationTaster	Benign	0.57	D;D;D
PrimateAI	Uncertain	0.69	T
PROVEAN	Benign	-0.83	N;N;N
REVEL	Benign	0.27
Sift	Benign	0.037	D;D;D
Sift4G	Benign	0.067	T;T;T
Polyphen		0.23	B;B;B
Vest4		0.28
MutPred		0.15		Loss of glycosylation at P161 (P = 0.0461);Loss of glycosylation at P161 (P = 0.0461);Loss of glycosylation at P161 (P = 0.0461);
MVP		0.65
MPC		0.75
ClinPred		0.32	T
GERP RS		1.8
Varity_R		0.23
gMVP		0.50

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: rs2335052; hg19: chr3-128204951;