rs13062436

Variant names:

• chr3-128498588-T-C
• rs13062436
• ENST00000468377.1:n.839-3021T>C

Variant summary

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

The ENST00000468377.1(GATA2-AS1):​n.839-3021T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,224 control chromosomes in the GnomAD database, including 2,015 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 0.14 (2015 hom., cov: 32)
• Consequence: GATA2-AS1 ENST00000468377.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 5 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000468377.1. 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
	GATA2-AS1	NR_125398.1		n.760-3021T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATA2-AS1	ENST00000468377.1	TSL:2	n.839-3021T>C		intron	N/A
	GATA2-AS1	ENST00000669945.1		n.294-3021T>C		intron	N/A
	GATA2-AS1	ENST00000740166.1		n.380+8519T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21598 AN: 152106 Hom.: 2010 Cov.: 32

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.142 AC: 21613 AN: 152224 Hom.: 2015 Cov.: 32 AF XY: 0.147 AC XY: 10958 AN XY: 74416

African (AFR) AF: 0.0438 AC: 1818 AN: 41544

American (AMR) AF: 0.199 AC: 3046 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3470

East Asian (EAS) AF: 0.384 AC: 1987 AN: 5168

South Asian (SAS) AF: 0.180 AC: 868 AN: 4830

European-Finnish (FIN) AF: 0.182 AC: 1926 AN: 10604

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10616 AN: 67998

Other (OTH) AF: 0.156 AC: 329 AN: 2110

Alfa AF: 0.140 Hom.: 1147

Bravo AF: 0.143

Asia WGS AF: 0.225 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.80
PhyloP100		-0.027
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs13062436;

hg19: chr3-128217431;