rs204938

chr11-8256650-C-T

Variant summary

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

The NM_002315.3(LMO1):c.25+6688G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,104 control chromosomes in the GnomAD database, including 20,116 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 0.49 (20116 hom., cov: 33)
• Consequence: LMO1 NM_002315.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMO1	NM_002315.3	c.25+6688G>A		intron_variant		ENST00000335790.8
LMO1	NM_001270428.2	c.22+11777G>A		intron_variant
LMO1	XM_011520099.3	c.-9+6108G>A		intron_variant
LMO1	NR_073006.2	n.541+6688G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMO1	ENST00000335790.8	c.25+6688G>A		intron_variant		1	NM_002315.3	A1
LMO1	ENST00000428101.6	c.22+11777G>A		intron_variant		1		P4
LMO1	ENST00000524379.1	n.51+6688G>A		intron_variant, non_coding_transcript_variant		1
LMO1	ENST00000534484.1	c.-9+7022G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75053 AN: 151986 Hom.: 20123 Cov.: 33

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.494 AC: 75066 AN: 152104 Hom.: 20116 Cov.: 33 AF XY: 0.503 AC XY: 37416 AN XY: 74352

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.526

Alfa AF: 0.548 Hom.: 30406

Bravo AF: 0.484

Asia WGS AF: 0.613 AC: 2130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.9
Dann	Benign	0.43

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: rs204938; hg19: chr11-8278197;