rs13386897

Positions:

• chr2-236190767-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000415226.1(GBX2-AS1):​n.223+23098A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GBX2-AS1	ENST00000415226.1	n.223+23098A>G		intron_variant, non_coding_transcript_variant		4
GBX2-AS1	ENST00000483218.1	n.206-22896A>G		intron_variant, non_coding_transcript_variant		3
GBX2-AS1	ENST00000686834.1	n.228+23098A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0726

Gnomad4 AMR AF: 0.0647

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.111

Alfa AF: 0.118 Hom.: 1422

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
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13386897; hg19: chr2-237099410;