rs204926

chr11-8233559-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002315.3(LMO1):c.26-3055C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,002 control chromosomes in the GnomAD database, including 15,087 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 0.41 (15087 hom., cov: 31)
• Consequence: LMO1 NM_002315.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.34

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMO1	NM_002315.3	c.26-3055C>T		intron_variant		ENST00000335790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMO1	ENST00000335790.8	c.26-3055C>T		intron_variant		1	NM_002315.3	A1
LMO1	ENST00000428101.6	c.23-3055C>T		intron_variant		1		P4
LMO1	ENST00000524379.1	n.52-3055C>T		intron_variant, non_coding_transcript_variant		1
LMO1	ENST00000534484.1	c.-8-3055C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62414 AN: 151884 Hom.: 15086 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.411 AC: 62432 AN: 152002 Hom.: 15087 Cov.: 31 AF XY: 0.416 AC XY: 30937 AN XY: 74296

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.452

Alfa AF: 0.496 Hom.: 15853

Bravo AF: 0.394

Asia WGS AF: 0.368 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.027
Dann	Benign	0.31

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: rs204926; hg19: chr11-8255106;