rs110419

Variant names:

• chr11-8231306-A-G
• rs110419
• NM_002315.3:c.26-802T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-8231306-A-G
• chr11-8231306-A-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.26-802T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,202 control chromosomes in the GnomAD database, including 15,530 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 0.43 (15530 hom., cov: 34)
• Consequence: LMO1 NM_002315.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.676
• Publications: 54 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]

LOC105376536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMO1	NM_002315.3	c.26-802T>C		intron_variant	Intron 1 of 3	ENST00000335790.8	NP_002306.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMO1	ENST00000335790.8	c.26-802T>C		intron_variant	Intron 1 of 3	1	NM_002315.3	ENSP00000338207.3
LMO1	ENST00000428101.6	c.23-802T>C		intron_variant	Intron 1 of 3	1		ENSP00000404538.2
LMO1	ENST00000524379.1	n.52-802T>C		intron_variant	Intron 1 of 3	1
LMO1	ENST00000534484.1	c.-8-802T>C		intron_variant	Intron 1 of 3	5		ENSP00000435456.1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65201 AN: 152084 Hom.: 15533 Cov.: 34

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.428 AC: 65199 AN: 152202 Hom.: 15530 Cov.: 34 AF XY: 0.435 AC XY: 32391 AN XY: 74404

African (AFR) AF: 0.202 AC: 8397 AN: 41546

American (AMR) AF: 0.522 AC: 7990 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1566 AN: 3472

East Asian (EAS) AF: 0.426 AC: 2199 AN: 5164

South Asian (SAS) AF: 0.689 AC: 3326 AN: 4826

European-Finnish (FIN) AF: 0.488 AC: 5175 AN: 10614

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34896 AN: 67974

Other (OTH) AF: 0.452 AC: 951 AN: 2106

Alfa AF: 0.488 Hom.: 76638

Bravo AF: 0.414

Asia WGS AF: 0.479 AC: 1666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.8
DANN	Benign	0.38
PhyloP100		0.68
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: rs110419; hg19: chr11-8252853;