rs678741

Variant names:

• chr10-101237824-G-A
• rs678741
• ENST00000546988.3:n.420-115G>A

Variant summary

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

The ENST00000546988.3(LBX1-AS1):​n.420-115G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 389,062 control chromosomes in the GnomAD database, including 60,241 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 0.51 (20656 hom., cov: 34)
  • Exomes 𝑓: 0.57 (39585 hom.)
• Consequence: LBX1-AS1 ENST00000546988.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 21 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LBX1-AS1	NR_029380.1	n.403-115G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LBX1-AS1	ENST00000546988.3	n.420-115G>A		intron_variant	Intron 2 of 2	1
LBX1-AS1	ENST00000430651.2	n.1643+114G>A		intron_variant	Intron 1 of 1	2
LBX1-AS1	ENST00000454527.2	n.184-115G>A		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77948 AN: 151988 Hom.: 20650 Cov.: 34

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.543

GnomAD4 exome AF: 0.572 AC: 135620 AN: 236956 Hom.: 39585 Cov.: 0 AF XY: 0.581 AC XY: 78137 AN XY: 134522

African (AFR) AF: 0.371 AC: 2188 AN: 5896

American (AMR) AF: 0.654 AC: 9633 AN: 14722

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 3452 AN: 6306

East Asian (EAS) AF: 0.473 AC: 4153 AN: 8778

South Asian (SAS) AF: 0.667 AC: 30128 AN: 45198

European-Finnish (FIN) AF: 0.583 AC: 5569 AN: 9556

Middle Eastern (MID) AF: 0.629 AC: 1517 AN: 2412

European-Non Finnish (NFE) AF: 0.548 AC: 72684 AN: 132672

Other (OTH) AF: 0.552 AC: 6296 AN: 11416

GnomAD4 genome AF: 0.513 AC: 77973 AN: 152106 Hom.: 20656 Cov.: 34 AF XY: 0.520 AC XY: 38674 AN XY: 74346

African (AFR) AF: 0.382 AC: 15845 AN: 41492

American (AMR) AF: 0.614 AC: 9379 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1865 AN: 3466

East Asian (EAS) AF: 0.462 AC: 2390 AN: 5178

South Asian (SAS) AF: 0.676 AC: 3261 AN: 4824

European-Finnish (FIN) AF: 0.597 AC: 6315 AN: 10574

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36983 AN: 67970

Other (OTH) AF: 0.543 AC: 1146 AN: 2112

Alfa AF: 0.519 Hom.: 3888

Bravo AF: 0.503

Asia WGS AF: 0.581 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.52
PhyloP100		0.037

Splicing

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

Other links and lift over

dbSNP: rs678741; hg19: chr10-102997581;