rs1322331

Variant names:

• chr10-101226832-A-C
• rs1322331
• NM_006562.5:c.*438T>G

Your query was ambiguous. Multiple possible variants found:

• chr10-101226832-A-C
• chr10-101226832-A-G
• chr10-101226832-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006562.5(LBX1):​c.*438T>G variant causes a downstream gene 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 NM_006562.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LBX1	NM_006562.5	c.*438T>G		downstream_gene_variant		ENST00000370193.4	NP_006553.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LBX1	ENST00000370193.4	c.*438T>G		downstream_gene_variant		1	NM_006562.5	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

Gnomad4 AFR exome AF: 0.733

Gnomad4 AMR exome AF: 0.231

Gnomad4 ASJ exome AF: 0.441

Gnomad4 EAS exome AF: 0.321

Gnomad4 SAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.643

Gnomad4 NFE exome AF: 0.444

Gnomad4 OTH exome AF: 0.632

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

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.467

Alfa AF: 0.457 Hom.: 19690

Bravo AF: 0.504

Asia WGS AF: 0.430 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1322331; hg19: chr10-102986589;