rs4237770

Variant names:

• chr11-8254288-T-C
• rs4237770
• NM_002315.3:c.25+9050A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-8254288-T-C
• chr11-8254288-T-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_002315.3(LMO1):​c.25+9050A>G variant causes a intron change. The variant allele was found at a frequency of 0.373 in 152,130 control chromosomes in the GnomAD database, including 12,507 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 0.37 (12507 hom., cov: 33)
• Consequence: LMO1 NM_002315.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.67
• Publications: 4 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMO1	NM_002315.3	c.25+9050A>G		intron_variant	Intron 1 of 3	ENST00000335790.8	NP_002306.1
LMO1	NM_001270428.2	c.22+14139A>G		intron_variant	Intron 1 of 3		NP_001257357.1
LMO1	NR_073006.2	n.541+9050A>G		intron_variant	Intron 1 of 3
LMO1	XM_011520099.3	c.-9+8470A>G		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.25+9050A>G		intron_variant	Intron 1 of 3	1	NM_002315.3	ENSP00000338207.3
LMO1	ENST00000428101.6	c.22+14139A>G		intron_variant	Intron 1 of 3	1		ENSP00000404538.2
LMO1	ENST00000524379.1	n.51+9050A>G		intron_variant	Intron 1 of 3	1
LMO1	ENST00000534484.1	c.-9+9384A>G		intron_variant	Intron 1 of 3	5		ENSP00000435456.1

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56752 AN: 152012 Hom.: 12512 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.373 AC: 56744 AN: 152130 Hom.: 12507 Cov.: 33 AF XY: 0.378 AC XY: 28102 AN XY: 74374

African (AFR) AF: 0.110 AC: 4573 AN: 41524

American (AMR) AF: 0.449 AC: 6866 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1808 AN: 3468

East Asian (EAS) AF: 0.498 AC: 2578 AN: 5174

South Asian (SAS) AF: 0.471 AC: 2271 AN: 4822

European-Finnish (FIN) AF: 0.467 AC: 4931 AN: 10566

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32205 AN: 67970

Other (OTH) AF: 0.405 AC: 856 AN: 2116

Alfa AF: 0.449 Hom.: 20650

Bravo AF: 0.362

Asia WGS AF: 0.428 AC: 1486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	22
DANN	Benign	0.80
PhyloP100		5.7
Mutation Taster		=99/1	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: rs4237770; hg19: chr11-8275835;