10-101249045-G-A

Position:

• chr10-101249045-G-A

Variant summary

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

The ENST00000434878.1(LBX1-AS1):​n.110+10998G>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 0.615 in 151,938 control chromosomes in the GnomAD database, including 28,924 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 0.61 (28924 hom., cov: 31)
• Consequence: LBX1-AS1 ENST00000434878.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LBX1-AS1	ENST00000434878.1	n.110+10998G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93381 AN: 151820 Hom.: 28907 Cov.: 31

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.615 AC: 93437 AN: 151938 Hom.: 28924 Cov.: 31 AF XY: 0.608 AC XY: 45103 AN XY: 74234

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.616

Alfa AF: 0.618 Hom.: 39216

Bravo AF: 0.610

Asia WGS AF: 0.530 AC: 1842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1885517; hg19: chr10-103008802;