11-8242602-G-A

Variant names:

• chr11-8242602-G-A
• rs442264
• NM_002315.3:c.26-12098C>T

Variant summary

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

The NM_002315.3(LMO1):​c.26-12098C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,052 control chromosomes in the GnomAD database, including 16,868 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 0.45 (16868 hom., cov: 33)
• Consequence: LMO1 NM_002315.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 9 publications found

Genes affected

LMO1 (HGNC:6641): (LIM domain only 1) This locus encodes a transcriptional regulator that contains two cysteine-rich LIM domains but lacks a DNA-binding domain. LIM domains may play a role in protein interactions; thus the encoded protein may regulate transcription by competitively binding to specific DNA-binding transcription factors. Alterations at this locus have been associated with acute lymphoblastic T-cell leukemia. Chromosomal rearrangements have been observed between this locus and at least two loci, the delta subunit of the T-cell antigen receptor gene and the LIM domain binding 1 gene. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMO1	NM_002315.3	c.26-12098C>T		intron_variant	Intron 1 of 3	ENST00000335790.8	NP_002306.1
LMO1	NM_001270428.2	c.23-12098C>T		intron_variant	Intron 1 of 3		NP_001257357.1
LMO1	NR_073006.2	n.542-12098C>T		intron_variant	Intron 1 of 3
LMO1	XM_011520099.3	c.-8-12098C>T		intron_variant	Intron 1 of 3		XP_011518401.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMO1	ENST00000335790.8	c.26-12098C>T		intron_variant	Intron 1 of 3	1	NM_002315.3	ENSP00000338207.3
LMO1	ENST00000428101.6	c.23-12098C>T		intron_variant	Intron 1 of 3	1		ENSP00000404538.2
LMO1	ENST00000524379.1	n.52-12098C>T		intron_variant	Intron 1 of 3	1
LMO1	ENST00000534484.1	c.-8-12098C>T		intron_variant	Intron 1 of 3	5		ENSP00000435456.1

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68614 AN: 151934 Hom.: 16850 Cov.: 33

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.452 AC: 68676 AN: 152052 Hom.: 16868 Cov.: 33 AF XY: 0.462 AC XY: 34328 AN XY: 74322

African (AFR) AF: 0.296 AC: 12284 AN: 41456

American (AMR) AF: 0.625 AC: 9564 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1761 AN: 3466

East Asian (EAS) AF: 0.856 AC: 4405 AN: 5146

South Asian (SAS) AF: 0.701 AC: 3374 AN: 4816

European-Finnish (FIN) AF: 0.450 AC: 4757 AN: 10582

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30902 AN: 67974

Other (OTH) AF: 0.483 AC: 1020 AN: 2110

Alfa AF: 0.451 Hom.: 2457

Bravo AF: 0.455

Asia WGS AF: 0.682 AC: 2371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.9
DANN	Benign	0.53
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs442264; hg19: chr11-8264149;