rs10883597

Variant names:

• chr10-101239997-C-T
• rs10883597
• ENST00000546988.3:n.2478C>T

Variant summary

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

The ENST00000546988.3(LBX1-AS1):​n.2478C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,946 control chromosomes in the GnomAD database, including 11,223 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 0.38 (11223 hom., cov: 32)
• Consequence: LBX1-AS1 ENST00000546988.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102
• Publications: 6 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546988.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LBX1-AS1	ENST00000546988.3	TSL:1	n.2478C>T		non_coding_transcript_exon	Exon 3 of 3
	LBX1-AS1	ENST00000434878.1	TSL:5	n.110+1950C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57709 AN: 151828 Hom.: 11217 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.380 AC: 57742 AN: 151946 Hom.: 11223 Cov.: 32 AF XY: 0.375 AC XY: 27866 AN XY: 74262

African (AFR) AF: 0.349 AC: 14455 AN: 41440

American (AMR) AF: 0.329 AC: 5029 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1338 AN: 3468

East Asian (EAS) AF: 0.542 AC: 2784 AN: 5140

South Asian (SAS) AF: 0.239 AC: 1151 AN: 4818

European-Finnish (FIN) AF: 0.381 AC: 4020 AN: 10548

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27768 AN: 67928

Other (OTH) AF: 0.381 AC: 804 AN: 2108

Alfa AF: 0.390 Hom.: 5039

Bravo AF: 0.382

Asia WGS AF: 0.353 AC: 1228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.4
DANN	Benign	0.48
PhyloP100		0.10

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10883597;

hg19: chr10-102999754;

COSMIC: COSV70416369;