1-225402941-A-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002296.4(LBR):c.*362T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
LBR
NM_002296.4 3_prime_UTR
NM_002296.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.893
Publications
0 publications found
Genes affected
LBR (HGNC:6518): (lamin B receptor) The protein encoded by this gene belongs to the ERG4/ERG24 family. It localized in the nuclear envelope inner membrane and anchors the lamina and the heterochromatin to the membrane. It may mediate interaction between chromatin and lamin B. Mutations of this gene has been associated with autosomal recessive HEM/Greenberg skeletal dysplasia. Alternative splicing occurs at this locus and two transcript variants encoding the same protein have been identified. [provided by RefSeq, Jul 2008]
LBR Gene-Disease associations (from GenCC):
- Greenberg dysplasiaInheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen, Orphanet, Ambry Genetics
- Pelger-Huet anomalyInheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- regressive spondylometaphyseal dysplasiaInheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_002296.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LBR | TSL:1 MANE Select | c.*362T>G | 3_prime_UTR | Exon 14 of 14 | ENSP00000272163.4 | Q14739 | |||
| LBR | TSL:5 | c.*362T>G | 3_prime_UTR | Exon 14 of 14 | ENSP00000339883.2 | Q14739 | |||
| LBR | c.*362T>G | 3_prime_UTR | Exon 14 of 14 | ENSP00000555854.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 43900Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 23128
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
43900
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
23128
African (AFR)
AF:
AC:
0
AN:
864
American (AMR)
AF:
AC:
0
AN:
2850
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
1052
East Asian (EAS)
AF:
AC:
0
AN:
2148
South Asian (SAS)
AF:
AC:
0
AN:
5732
European-Finnish (FIN)
AF:
AC:
0
AN:
1772
Middle Eastern (MID)
AF:
AC:
0
AN:
148
European-Non Finnish (NFE)
AF:
AC:
0
AN:
26854
Other (OTH)
AF:
AC:
0
AN:
2480
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
Greenberg dysplasia (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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
Publications
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