rs625039

Variant names:

• chr10-101233892-G-A
• rs625039
• ENST00000546988.3:n.419+1458G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-101233892-G-A
• chr10-101233892-G-T

Variant summary

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

The ENST00000546988.3(LBX1-AS1):​n.419+1458G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,970 control chromosomes in the GnomAD database, including 4,512 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 0.22 (4512 hom., cov: 32)
• Consequence: LBX1-AS1 ENST00000546988.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.966
• Publications: 13 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=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546988.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LBX1-AS1	NR_029380.1		n.402+1458G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LBX1-AS1	ENST00000546988.3	TSL:1	n.419+1458G>A		intron	N/A
	LBX1-AS1	ENST00000454527.2	TSL:5	n.183+1458G>A		intron	N/A
	LBX1-AS1	ENST00000823572.1		n.273+1458G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32767 AN: 151854 Hom.: 4507 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.0962

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.216 AC: 32797 AN: 151970 Hom.: 4512 Cov.: 32 AF XY: 0.214 AC XY: 15872 AN XY: 74282

African (AFR) AF: 0.374 AC: 15487 AN: 41366

American (AMR) AF: 0.172 AC: 2635 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 756 AN: 3472

East Asian (EAS) AF: 0.368 AC: 1902 AN: 5166

South Asian (SAS) AF: 0.219 AC: 1051 AN: 4798

European-Finnish (FIN) AF: 0.0962 AC: 1019 AN: 10596

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.138 AC: 9385 AN: 67984

Other (OTH) AF: 0.196 AC: 414 AN: 2110

Alfa AF: 0.168 Hom.: 8117

Bravo AF: 0.231

Asia WGS AF: 0.275 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	10
DANN	Benign	0.65
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs625039; hg19: chr10-102993649;