rs4237770

chr11-8254288-T-Cchr11-8254288-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LMO1	NM_002315.3	c.25+9050A>G		intron_variant		ENST00000335790.8
LMO1	NM_001270428.2	c.22+14139A>G		intron_variant
LMO1	XM_011520099.3	c.-9+8470A>G		intron_variant
LMO1	NR_073006.2	n.541+9050A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMO1	ENST00000335790.8	c.25+9050A>G		intron_variant		1	NM_002315.3	A1
LMO1	ENST00000428101.6	c.22+14139A>G		intron_variant		1		P4
LMO1	ENST00000524379.1	n.51+9050A>G		intron_variant, non_coding_transcript_variant		1
LMO1	ENST00000534484.1	c.-9+9384A>G		intron_variant		5

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

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.405

Alfa AF: 0.464 Hom.: 16523

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs4237770; hg19: chr11-8275835;