rs442264

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002315.3(LMO1):​c.26-12098C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,052 control chromosomes in the GnomAD database, including 16,868 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 0.45 ( 16868 hom., cov: 33)

Consequence

LMO1
NM_002315.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.123
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LMO1NM_002315.3 linkuse as main transcriptc.26-12098C>T intron_variant ENST00000335790.8 NP_002306.1
LMO1NM_001270428.2 linkuse as main transcriptc.23-12098C>T intron_variant NP_001257357.1
LMO1XM_011520099.3 linkuse as main transcriptc.-8-12098C>T intron_variant XP_011518401.1
LMO1NR_073006.2 linkuse as main transcriptn.542-12098C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LMO1ENST00000335790.8 linkuse as main transcriptc.26-12098C>T intron_variant 1 NM_002315.3 ENSP00000338207 A1P25800-1
LMO1ENST00000428101.6 linkuse as main transcriptc.23-12098C>T intron_variant 1 ENSP00000404538 P4P25800-2
LMO1ENST00000524379.1 linkuse as main transcriptn.52-12098C>T intron_variant, non_coding_transcript_variant 1
LMO1ENST00000534484.1 linkuse as main transcriptc.-8-12098C>T intron_variant 5 ENSP00000435456

Frequencies

GnomAD3 genomes
AF:
0.452
AC:
68614
AN:
151934
Hom.:
16850
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.296
Gnomad AMI
AF:
0.502
Gnomad AMR
AF:
0.624
Gnomad ASJ
AF:
0.508
Gnomad EAS
AF:
0.857
Gnomad SAS
AF:
0.701
Gnomad FIN
AF:
0.450
Gnomad MID
AF:
0.516
Gnomad NFE
AF:
0.455
Gnomad OTH
AF:
0.481
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.452
AC:
68676
AN:
152052
Hom.:
16868
Cov.:
33
AF XY:
0.462
AC XY:
34328
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.296
Gnomad4 AMR
AF:
0.625
Gnomad4 ASJ
AF:
0.508
Gnomad4 EAS
AF:
0.856
Gnomad4 SAS
AF:
0.701
Gnomad4 FIN
AF:
0.450
Gnomad4 NFE
AF:
0.455
Gnomad4 OTH
AF:
0.483
Alfa
AF:
0.451
Hom.:
2457
Bravo
AF:
0.455
Asia WGS
AF:
0.682
AC:
2371
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
3.9
DANN
Benign
0.53

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs442264; hg19: chr11-8264149; API