rs11190878

Positions:

• chr10-101250151-A-G

Variant summary

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

The ENST00000434878.1(LBX1-AS1):​n.110+12104A>G 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 0.209 in 152,134 control chromosomes in the GnomAD database, including 4,176 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 0.21 (4176 hom., cov: 31)
• Consequence: LBX1-AS1 ENST00000434878.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 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+12104A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31844 AN: 152016 Hom.: 4174 Cov.: 31

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.0457

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.209 AC: 31841 AN: 152134 Hom.: 4176 Cov.: 31 AF XY: 0.207 AC XY: 15377 AN XY: 74358

Gnomad4 AFR AF: 0.0874

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.0460

Gnomad4 SAS AF: 0.0969

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.203

Alfa AF: 0.255 Hom.: 2858

Bravo AF: 0.194

Asia WGS AF: 0.0720 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11190878; hg19: chr10-103009908;