chr10-101239262-A-G

Variant names:

• chr10-101239262-A-G
• rs12773591
• ENST00000546988.3:n.1743A>G

Variant summary

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

The ENST00000546988.3(LBX1-AS1):​n.1743A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,122 control chromosomes in the GnomAD database, including 3,582 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 (3582 hom., cov: 32)
• Consequence: LBX1-AS1 ENST00000546988.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.276 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LBX1-AS1	ENST00000546988.3	TSL:1	n.1743A>G		non_coding_transcript_exon	Exon 3 of 3
	LBX1-AS1	ENST00000434878.1	TSL:5	n.110+1215A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29629 AN: 152004 Hom.: 3580 Cov.: 32

Gnomad AFR AF: 0.0798

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0524

Gnomad SAS AF: 0.0845

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.195 AC: 29633 AN: 152122 Hom.: 3582 Cov.: 32 AF XY: 0.191 AC XY: 14190 AN XY: 74354

African (AFR) AF: 0.0797 AC: 3310 AN: 41520

American (AMR) AF: 0.179 AC: 2730 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3470

East Asian (EAS) AF: 0.0527 AC: 273 AN: 5180

South Asian (SAS) AF: 0.0850 AC: 410 AN: 4824

European-Finnish (FIN) AF: 0.247 AC: 2605 AN: 10566

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19010 AN: 67956

Other (OTH) AF: 0.195 AC: 412 AN: 2112

Alfa AF: 0.217 Hom.: 1442

Bravo AF: 0.187

Asia WGS AF: 0.0720 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.6
DANN	Benign	0.55
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs12773591; hg19: chr10-102999019;