rs11593547

chr10-101241298-C-T

Variant summary

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

The ENST00000434878.1(LBX1-AS1):n.110+3251C>T 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 0.192 in 152,116 control chromosomes in the GnomAD database, including 3,732 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 (3732 hom., cov: 33)
• Consequence: LBX1-AS1 ENST00000434878.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 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	ENST00000434878.1	n.110+3251C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29229 AN: 151998 Hom.: 3729 Cov.: 33

Gnomad AFR AF: 0.0570

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0457

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.192 AC: 29226 AN: 152116 Hom.: 3732 Cov.: 33 AF XY: 0.190 AC XY: 14142 AN XY: 74350

Gnomad4 AFR AF: 0.0569

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.0460

Gnomad4 SAS AF: 0.0987

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.188

Alfa AF: 0.244 Hom.: 628

Bravo AF: 0.176

Asia WGS AF: 0.0710 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.88
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11593547; hg19: chr10-103001055;