rs11593547

Variant names:

• chr10-101241298-C-T
• rs11593547
• ENST00000434878.1:n.110+3251C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000434878.1(LBX1-AS1):​n.110+3251C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LBX1-AS1	ENST00000434878.1	n.110+3251C>T		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.0569 AC: 2362 AN: 41526

American (AMR) AF: 0.162 AC: 2471 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 633 AN: 3470

East Asian (EAS) AF: 0.0460 AC: 238 AN: 5176

South Asian (SAS) AF: 0.0987 AC: 476 AN: 4822

European-Finnish (FIN) AF: 0.296 AC: 3128 AN: 10562

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19350 AN: 67948

Other (OTH) AF: 0.188 AC: 398 AN: 2116

Alfa AF: 0.236 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
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs11593547; hg19: chr10-103001055;