rs56325233

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-128533470-C-A
• chr3-128533470-C-G
• chr3-128533470-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000740166.1(GATA2-AS1):​n.381-4542C>A 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 0.042 (8 hom., cov: 0)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0416 AC: 1801 AN: 43294 Hom.: 8 Cov.: 0

Gnomad AFR AF: 0.0214

Gnomad AMI AF: 0.0727

Gnomad AMR AF: 0.0206

Gnomad ASJ AF: 0.0705

Gnomad EAS AF: 0.0138

Gnomad SAS AF: 0.0503

Gnomad FIN AF: 0.0444

Gnomad MID AF: 0.0556

Gnomad NFE AF: 0.0705

Gnomad OTH AF: 0.0317

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0416 AC: 1801 AN: 43326 Hom.: 8 Cov.: 0 AF XY: 0.0389 AC XY: 809 AN XY: 20800

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0213 AC: 365 AN: 17134

American (AMR) AF: 0.0208 AC: 93 AN: 4480

Ashkenazi Jewish (ASJ) AF: 0.0705 AC: 66 AN: 936

East Asian (EAS) AF: 0.0138 AC: 26 AN: 1884

South Asian (SAS) AF: 0.0497 AC: 55 AN: 1106

European-Finnish (FIN) AF: 0.0444 AC: 59 AN: 1330

Middle Eastern (MID) AF: 0.0588 AC: 4 AN: 68

European-Non Finnish (NFE) AF: 0.0705 AC: 1098 AN: 15564

Other (OTH) AF: 0.0315 AC: 19 AN: 604

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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	-0.91
CADD	Benign	3.1
DANN	Benign	0.51
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs56325233; hg19: chr3-128252313;