10-101233892-G-A

Position:

• chr10-101233892-G-A

Variant summary

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

The NR_029380.1(LBX1-AS1):​n.402+1458G>A variant causes a intron, non coding transcript 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 NR_029380.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.966

Genes affected

LBX1-AS1 (HGNC:48678): (LBX1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LBX1-AS1	NR_029380.1	n.402+1458G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LBX1-AS1	ENST00000546988.3	n.419+1458G>A		intron_variant, non_coding_transcript_variant		1
LBX1-AS1	ENST00000454527.2	n.183+1458G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.0962

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.196

Alfa AF: 0.156 Hom.: 4236

Bravo AF: 0.231

Asia WGS AF: 0.275 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs625039; hg19: chr10-102993649;