10-101226832-A-C

Variant names:

• chr10-101226832-A-C
• rs1322331
• ENST00000945825.1:c.*438T>G

Variant summary

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

The ENST00000945825.1(LBX1):​c.*438T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,472 control chromosomes in the GnomAD database, including 19,304 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 0.50 (19228 hom., cov: 32)
  • Exomes 𝑓: 0.46 (76 hom.)
• Consequence: LBX1 ENST00000945825.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 10 publications found

Genes affected

LBX1 (HGNC:16960): (ladybird homeobox 1) This gene and the orthologous mouse gene were found by their homology to the Drosophila lady bird early and late homeobox genes. In the mouse, this gene is a key regulator of muscle precursor cell migration and is required for the acquisition of dorsal identities of forelimb muscles. [provided by RefSeq, Jul 2008]

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000945825.1. 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	NM_006562.5	MANE Select	c.*438T>G		downstream_gene	N/A	NP_006553.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LBX1	ENST00000945825.1		c.*438T>G		3_prime_UTR	Exon 3 of 3	ENSP00000615884.1
	LBX1-AS1	ENST00000823572.1		n.92+4940A>C		intron	N/A
	LBX1	ENST00000370193.4	TSL:1 MANE Select	c.*438T>G		downstream_gene	N/A	ENSP00000359212.2

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75068 AN: 151672 Hom.: 19197 Cov.: 32

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.467

GnomAD4 exome AF: 0.456 AC: 312 AN: 684 Hom.: 76 Cov.: 0 AF XY: 0.435 AC XY: 154 AN XY: 354

African (AFR) AF: 0.733 AC: 22 AN: 30

American (AMR) AF: 0.231 AC: 6 AN: 26

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 15 AN: 34

East Asian (EAS) AF: 0.321 AC: 9 AN: 28

South Asian (SAS) AF: 0.333 AC: 4 AN: 12

European-Finnish (FIN) AF: 0.643 AC: 9 AN: 14

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.444 AC: 222 AN: 500

Other (OTH) AF: 0.632 AC: 24 AN: 38

GnomAD4 genome AF: 0.495 AC: 75151 AN: 151788 Hom.: 19228 Cov.: 32 AF XY: 0.487 AC XY: 36143 AN XY: 74166

African (AFR) AF: 0.620 AC: 25668 AN: 41368

American (AMR) AF: 0.392 AC: 5977 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1582 AN: 3470

East Asian (EAS) AF: 0.581 AC: 2991 AN: 5148

South Asian (SAS) AF: 0.334 AC: 1600 AN: 4788

European-Finnish (FIN) AF: 0.405 AC: 4265 AN: 10534

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.466 AC: 31654 AN: 67926

Other (OTH) AF: 0.467 AC: 983 AN: 2106

Alfa AF: 0.472 Hom.: 58814

Bravo AF: 0.504

Asia WGS AF: 0.430 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	9.9
DANN	Benign	0.56
PhyloP100		-0.021

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1322331; hg19: chr10-102986589;