rs13062436

chr3-128498588-T-C

Variant summary

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

The NR_125398.1(GATA2-AS1):n.760-3021T>C variant causes a intron, non coding transcript 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 NR_125398.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

Genes affected

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GATA2-AS1	NR_125398.1	n.760-3021T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GATA2-AS1	ENST00000669945.1	n.294-3021T>C		intron_variant, non_coding_transcript_variant
GATA2-AS1	ENST00000468377.1	n.839-3021T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0438

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.156

Alfa AF: 0.154 Hom.: 658

Bravo AF: 0.143

Asia WGS AF: 0.225 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.1
Dann	Benign	0.80
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

Publications

LitVar

Other links and lift over

dbSNP: rs13062436; hg19: chr3-128217431;