rs594791

chr10-101236039-T-Cchr10-101236039-T-G

Variant summary

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

The NR_029380.1(LBX1-AS1):n.403-1900T>C 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 0.548 in 150,158 control chromosomes in the GnomAD database, including 23,208 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 0.55 (23196 hom., cov: 26)
  • Exomes 𝑓: 0.62 (12 hom.)
• Consequence: LBX1-AS1 NR_029380.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LBX1-AS1	NR_029380.1	n.403-1900T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LBX1-AS1	ENST00000546988.3	n.420-1900T>C		intron_variant, non_coding_transcript_variant		1
LBX1-AS1	ENST00000454527.2	n.184-1900T>C		intron_variant, non_coding_transcript_variant		5
LBX1-AS1	ENST00000430651.1			upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.548 AC: 82257 AN: 149996 Hom.: 23189 Cov.: 26

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.576

GnomAD4 exome AF: 0.619 AC: 26 AN: 42 Hom.: 12 Cov.: 0 AF XY: 0.559 AC XY: 19 AN XY: 34

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 1.00

Gnomad4 FIN exome AF: 0.667

Gnomad4 NFE exome AF: 0.607

GnomAD4 genome AF: 0.548 AC: 82304 AN: 150116 Hom.: 23196 Cov.: 26 AF XY: 0.557 AC XY: 40820 AN XY: 73284

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.579

Alfa AF: 0.567 Hom.: 24025

Bravo AF: 0.533

Asia WGS AF: 0.648 AC: 2255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.3
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs594791; hg19: chr10-102995796;