rs12773591

chr10-101239262-A-Gchr10-101239262-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LBX1-AS1	ENST00000546988.3	n.1743A>G		non_coding_transcript_exon_variant	3/3	1
LBX1-AS1	ENST00000434878.1	n.110+1215A>G		intron_variant, non_coding_transcript_variant		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;