rs12773591

Variant names:

• chr10-101239262-A-G
• rs12773591
• ENST00000546988.3:n.1743A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-101239262-A-G
• chr10-101239262-A-T

Variant summary

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

The ENST00000546988.3(LBX1-AS1):​n.1743A>G 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 0.195 in 152,122 control chromosomes in the GnomAD database, including 3,582 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 0.19 (3582 hom., cov: 32)
• Consequence: LBX1-AS1 ENST00000546988.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

LBX1-AS1 (HGNC:48678): (LBX1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LBX1-AS1	ENST00000546988.3	n.1743A>G		non_coding_transcript_exon_variant	Exon 3 of 3	1
LBX1-AS1	ENST00000434878.1	n.110+1215A>G		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29629 AN: 152004 Hom.: 3580 Cov.: 32

Gnomad AFR AF: 0.0798

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0524

Gnomad SAS AF: 0.0845

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.195 AC: 29633 AN: 152122 Hom.: 3582 Cov.: 32 AF XY: 0.191 AC XY: 14190 AN XY: 74354

Gnomad4 AFR AF: 0.0797

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.0527

Gnomad4 SAS AF: 0.0850

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.195

Alfa AF: 0.201 Hom.: 766

Bravo AF: 0.187

Asia WGS AF: 0.0720 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12773591; hg19: chr10-102999019;