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
NM_002315.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.123
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]
Genome browser will be placed here
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 | UniProt |
---|---|---|---|---|---|---|---|
LMO1 | NM_002315.3 | c.26-12098C>T | intron_variant | ENST00000335790.8 | |||
LMO1 | NM_001270428.2 | c.23-12098C>T | intron_variant | ||||
LMO1 | XM_011520099.3 | c.-8-12098C>T | intron_variant | ||||
LMO1 | NR_073006.2 | n.542-12098C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMO1 | ENST00000335790.8 | c.26-12098C>T | intron_variant | 1 | NM_002315.3 | A1 | |||
LMO1 | ENST00000428101.6 | c.23-12098C>T | intron_variant | 1 | P4 | ||||
LMO1 | ENST00000524379.1 | n.52-12098C>T | intron_variant, non_coding_transcript_variant | 1 | |||||
LMO1 | ENST00000534484.1 | c.-8-12098C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.452 AC: 68614AN: 151934Hom.: 16850 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
68614
AN:
151934
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.452 AC: 68676AN: 152052Hom.: 16868 Cov.: 33 AF XY: 0.462 AC XY: 34328AN XY: 74322
GnomAD4 genome
?
AF:
AC:
68676
AN:
152052
Hom.:
Cov.:
33
AF XY:
AC XY:
34328
AN XY:
74322
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2371
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at