rs9854612

Variant names:

• chr3-128538371-G-A
• rs9854612
• ENST00000474255.1:n.352G>A

Variant summary

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

The ENST00000740166.1(GATA2-AS1):​n.740G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 583,758 control chromosomes in the GnomAD database, including 38,054 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 0.40 (13722 hom., cov: 32)
  • Exomes 𝑓: 0.32 (24332 hom.)
• Consequence: GATA2-AS1 ENST00000740166.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 6 publications found

Genes affected

TMED10P2 (HGNC:38105): (transmembrane p24 trafficking protein 10 pseudogene 2)

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=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 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
	TMED10P2	ENST00000474255.1	TSL:6	n.352G>A		non_coding_transcript_exon	Exon 1 of 1
	GATA2-AS1	ENST00000740166.1		n.740G>A		non_coding_transcript_exon	Exon 3 of 3
	GATA2-AS1	ENST00000740167.1		n.668G>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60914 AN: 151832 Hom.: 13688 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.395

GnomAD4 exome AF: 0.325 AC: 140241 AN: 431806 Hom.: 24332 Cov.: 6 AF XY: 0.321 AC XY: 75963 AN XY: 236434

African (AFR) AF: 0.605 AC: 6929 AN: 11448

American (AMR) AF: 0.437 AC: 11673 AN: 26698

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 4521 AN: 11112

East Asian (EAS) AF: 0.461 AC: 9307 AN: 20198

South Asian (SAS) AF: 0.301 AC: 16353 AN: 54240

European-Finnish (FIN) AF: 0.268 AC: 5343 AN: 19964

Middle Eastern (MID) AF: 0.424 AC: 1304 AN: 3072

European-Non Finnish (NFE) AF: 0.294 AC: 77541 AN: 263762

Other (OTH) AF: 0.341 AC: 7270 AN: 21312

GnomAD4 genome AF: 0.402 AC: 61011 AN: 151952 Hom.: 13722 Cov.: 32 AF XY: 0.400 AC XY: 29738 AN XY: 74264

African (AFR) AF: 0.601 AC: 24915 AN: 41438

American (AMR) AF: 0.425 AC: 6487 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1396 AN: 3468

East Asian (EAS) AF: 0.463 AC: 2393 AN: 5168

South Asian (SAS) AF: 0.305 AC: 1473 AN: 4822

European-Finnish (FIN) AF: 0.270 AC: 2854 AN: 10558

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.297 AC: 20195 AN: 67930

Other (OTH) AF: 0.397 AC: 836 AN: 2108

Alfa AF: 0.322 Hom.: 13384

Bravo AF: 0.427

Asia WGS AF: 0.398 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs9854612; hg19: chr3-128257214;