dbSNP rs13386897: GBX2-AS1:n.223+23098A>G (chr2-236190767-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000415226.1(GBX2-AS1):n.223+23098A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,208 control chromosomes in the GnomAD database, including 922 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 0.10 ( 922 hom., cov: 32)

Consequence

GBX2-AS1
ENST00000415226.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.257

Publications

6 publications found

Variant links:

Genes affected

GBX2-AS1 (HGNC:55714): (GBX2 and ASB18 antisense RNA 1)

GBX2-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=-0.98).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GBX2-AS1	NR_186035.1 link	n.229-22896A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
GBX2-AS1	ENST00000415226.1 link	n.223+23098A>G	intron_variant	Intron 1 of 3	4
GBX2-AS1	ENST00000483218.1 link	n.206-22896A>G	intron_variant	Intron 1 of 1	3
GBX2-AS1	ENST00000686834.2 link	n.260+23098A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15564

AN:

152090

Hom.:

915

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0719

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.0649

Gnomad ASJ

AF:

0.109

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.156

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.124

Gnomad OTH

AF:

0.112

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

GnomAD4 genome

AF:

0.102

AC:

15597

AN:

152208

Hom.:

922

Cov.:

AF XY:

0.103

AC XY:

7669

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.0726

AC:

3015

AN:

41544

American (AMR)

AF:

0.0647

AC:

990

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.109

AC:

379

AN:

3470

East Asian (EAS)

AF:

0.00212

AC:

AN:

5182

South Asian (SAS)

AF:

0.139

AC:

669

AN:

4816

European-Finnish (FIN)

AF:

0.156

AC:

1653

AN:

10602

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.124

AC:

8417

AN:

67978

Other (OTH)

AF:

0.111

AC:

235

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

713

1426

2139

2852

3565

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

376

564

752

940

<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:

0.112

Hom.:

1883

Bravo

AF:

0.0918

Asia WGS

AF:

0.0740

AC:

257

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

8.0

(source)

DANN

Benign

0.51

PhyloP100

0.26

Splicing

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

Publications

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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