Genetic Variant ENST00000740166.1:n.381-5177C>T (chr3-128532835-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000740166.1(GATA2-AS1):n.381-5177C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,918 control chromosomes in the GnomAD database, including 2,436 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 0.16 ( 2436 hom., cov: 31)

Consequence

GATA2-AS1
ENST00000740166.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20

Publications

4 publications found

Variant links:

Genes affected

GATA2-AS1 (HGNC:51108): (GATA2 antisense RNA 1)

GATA2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
GATA2-AS1	ENST00000740166.1 link	n.381-5177C>T	intron_variant	Intron 2 of 2
GATA2-AS1	ENST00000740167.1 link	n.346-5214C>T	intron_variant	Intron 2 of 2
GATA2-AS1	ENST00000740168.1 link	n.457-5177C>T	intron_variant	Intron 2 of 2
GATA2-AS1	ENST00000740169.1 link	n.434-5177C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.158

AC:

24029

AN:

151800

Hom.:

2431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0495

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.340

Gnomad SAS

AF:

0.235

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.182

Gnomad OTH

AF:

0.158

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

GnomAD4 genome

AF:

0.158

AC:

24042

AN:

151918

Hom.:

2436

Cov.:

AF XY:

0.164

AC XY:

12137

AN XY:

74202

show subpopulations

African (AFR)

AF:

0.0494

AC:

2050

AN:

41462

American (AMR)

AF:

0.211

AC:

3227

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.236

AC:

817

AN:

3466

East Asian (EAS)

AF:

0.339

AC:

1741

AN:

5130

South Asian (SAS)

AF:

0.235

AC:

1130

AN:

4804

European-Finnish (FIN)

AF:

0.200

AC:

2111

AN:

10530

Middle Eastern (MID)

AF:

0.184

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.182

AC:

12372

AN:

67934

Other (OTH)

AF:

0.161

AC:

339

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

988

1975

2963

3950

4938

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

270

540

810

1080

1350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.147

Hom.:

764

Bravo

AF:

0.156

Asia WGS

AF:

0.243

AC:

846

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.9

(source)

DANN

Benign

0.56

PhyloP100

-1.2

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over