3-128533470-C-G

Variant names:

• chr3-128533470-C-G
• rs56325233
• ENST00000740166.1:n.381-4542C>G

Variant summary

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

The ENST00000740166.1(GATA2-AS1):​n.381-4542C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.18 (896 hom., cov: 0)
• Consequence: GATA2-AS1 ENST00000740166.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459
• Publications: 6 publications found

Genes affected

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740166.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATA2-AS1	ENST00000740166.1		n.381-4542C>G		intron	N/A
	GATA2-AS1	ENST00000740167.1		n.346-4579C>G		intron	N/A
	GATA2-AS1	ENST00000740168.1		n.457-4542C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.182 AC: 8180 AN: 44892 Hom.: 895 Cov.: 0

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.0345

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.224

Gnomad NFE AF: 0.0695

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.182 AC: 8195 AN: 44920 Hom.: 896 Cov.: 0 AF XY: 0.189 AC XY: 4046 AN XY: 21434

African (AFR) AF: 0.295 AC: 5163 AN: 17490

American (AMR) AF: 0.185 AC: 847 AN: 4568

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 103 AN: 964

East Asian (EAS) AF: 0.241 AC: 463 AN: 1924

South Asian (SAS) AF: 0.121 AC: 138 AN: 1136

European-Finnish (FIN) AF: 0.146 AC: 200 AN: 1370

Middle Eastern (MID) AF: 0.236 AC: 17 AN: 72

European-Non Finnish (NFE) AF: 0.0695 AC: 1150 AN: 16540

Other (OTH) AF: 0.170 AC: 106 AN: 624

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.50
PhyloP100		0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs56325233;

hg19: chr3-128252313;