ENST00000415226.1:n.223+23098A>G

Variant names:

• chr2-236190767-A-G
• rs13386897
• ENST00000415226.1:n.223+23098A>G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 6 publications found

Genes affected

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415226.1. 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
	GBX2-AS1	NR_186035.1		n.229-22896A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GBX2-AS1	ENST00000415226.1	TSL:4	n.223+23098A>G		intron	N/A
	GBX2-AS1	ENST00000483218.1	TSL:3	n.206-22896A>G		intron	N/A
	GBX2-AS1	ENST00000686834.2		n.260+23098A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15564 AN: 152090 Hom.: 915 Cov.: 32

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.: 32 AF XY: 0.103 AC XY: 7669 AN XY: 74438

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: 11 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: 62 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8417 AN: 67978

Other (OTH) AF: 0.111 AC: 235 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	8.0
DANN	Benign	0.51
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs13386897; hg19: chr2-237099410;