10-101250151-A-G

Variant names:

• chr10-101250151-A-G
• rs11190878
• ENST00000434878.1:n.110+12104A>G

Variant summary

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

The ENST00000434878.1(LBX1-AS1):​n.110+12104A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 4 publications found

Genes affected

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=-0.92).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LBX1-AS1	ENST00000434878.1	n.110+12104A>G		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.0874 AC: 3630 AN: 41532

American (AMR) AF: 0.171 AC: 2617 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 657 AN: 3470

East Asian (EAS) AF: 0.0460 AC: 238 AN: 5176

South Asian (SAS) AF: 0.0969 AC: 467 AN: 4820

European-Finnish (FIN) AF: 0.304 AC: 3208 AN: 10558

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20379 AN: 67972

Other (OTH) AF: 0.203 AC: 429 AN: 2110

Alfa AF: 0.255 Hom.: 3169

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
PhyloP100		-0.052

Splicing

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

Other links and lift over

dbSNP: rs11190878; hg19: chr10-103009908;