rs4758317

Variant names:

• chr11-8229264-C-A
• rs4758317
• NM_002315.3:c.239+1027G>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.239+1027G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,976 control chromosomes in the GnomAD database, including 24,756 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 0.57 (24756 hom., cov: 32)
• Consequence: LMO1 NM_002315.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394
• Publications: 14 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]

ENSG00000307401 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMO1	NM_002315.3	c.239+1027G>T		intron_variant	Intron 2 of 3	ENST00000335790.8	NP_002306.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMO1	ENST00000335790.8	c.239+1027G>T		intron_variant	Intron 2 of 3	1	NM_002315.3	ENSP00000338207.3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86483 AN: 151858 Hom.: 24738 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.569 AC: 86543 AN: 151976 Hom.: 24756 Cov.: 32 AF XY: 0.571 AC XY: 42420 AN XY: 74256

African (AFR) AF: 0.592 AC: 24523 AN: 41456

American (AMR) AF: 0.591 AC: 9034 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1849 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2198 AN: 5174

South Asian (SAS) AF: 0.734 AC: 3526 AN: 4804

European-Finnish (FIN) AF: 0.511 AC: 5384 AN: 10532

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38041 AN: 67940

Other (OTH) AF: 0.576 AC: 1211 AN: 2104

Alfa AF: 0.568 Hom.: 31282

Bravo AF: 0.569

Asia WGS AF: 0.516 AC: 1795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.41
PhyloP100		-0.39
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: rs4758317; hg19: chr11-8250811;