rs1885517

Variant names:

• chr10-101249045-G-A
• rs1885517
• ENST00000434878.1:n.110+10998G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-101249045-G-A
• chr10-101249045-G-C
• chr10-101249045-G-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+10998G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,938 control chromosomes in the GnomAD database, including 28,924 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 0.61 (28924 hom., cov: 31)
• Consequence: LBX1-AS1 ENST00000434878.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 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+10998G>A		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93381 AN: 151820 Hom.: 28907 Cov.: 31

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.615 AC: 93437 AN: 151938 Hom.: 28924 Cov.: 31 AF XY: 0.608 AC XY: 45103 AN XY: 74234

African (AFR) AF: 0.647 AC: 26795 AN: 41428

American (AMR) AF: 0.491 AC: 7498 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2427 AN: 3472

East Asian (EAS) AF: 0.638 AC: 3278 AN: 5140

South Asian (SAS) AF: 0.459 AC: 2211 AN: 4816

European-Finnish (FIN) AF: 0.596 AC: 6277 AN: 10528

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43011 AN: 67972

Other (OTH) AF: 0.616 AC: 1304 AN: 2116

Alfa AF: 0.619 Hom.: 66860

Bravo AF: 0.610

Asia WGS AF: 0.530 AC: 1842 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	2.4
DANN	Benign	0.82
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1885517; hg19: chr10-103008802;