rs1435218
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001126328.3(LNX1):c.381-27505G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0888 in 152,236 control chromosomes in the GnomAD database, including 583 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association not found (★).
Frequency
Genomes: 𝑓 0.089 ( 583 hom., cov: 32)
Consequence
LNX1
NM_001126328.3 intron
NM_001126328.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.274
Publications
2 publications found
Genes affected
LNX1 (HGNC:6657): (ligand of numb-protein X 1) This gene encodes a membrane-bound protein that is involved in signal transduction and protein interactions. The encoded product is an E3 ubiquitin-protein ligase, which mediates ubiquitination and subsequent proteasomal degradation of proteins containing phosphotyrosine binding (PTB) domains. This protein may play an important role in tumorogenesis. Alternatively spliced transcript variants encoding distinct isoforms have been described. A pseudogene, which is located on chromosome 17, has been identified for this gene. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0975 is higher than 0.05.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LNX1 | NM_001126328.3 | c.381-27505G>A | intron_variant | Intron 2 of 10 | ENST00000263925.8 | NP_001119800.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| LNX1 | ENST00000263925.8 | c.381-27505G>A | intron_variant | Intron 2 of 10 | 1 | NM_001126328.3 | ENSP00000263925.7 | |||
| ENSG00000282278 | ENST00000507166.5 | c.1017+109767C>T | intron_variant | Intron 12 of 23 | 2 | ENSP00000423325.1 |
Frequencies
GnomAD3 genomes 0.0888 AC: 13507AN: 152118Hom.: 580 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
13507
AN:
152118
Hom.:
Cov.:
32
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 0.0888 AC: 13524AN: 152236Hom.: 583 Cov.: 32 AF XY: 0.0857 AC XY: 6380AN XY: 74432 show subpopulations
GnomAD4 genome
AF:
AC:
13524
AN:
152236
Hom.:
Cov.:
32
AF XY:
AC XY:
6380
AN XY:
74432
show subpopulations
African (AFR)
AF:
AC:
3629
AN:
41556
American (AMR)
AF:
AC:
994
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
AC:
252
AN:
3470
East Asian (EAS)
AF:
AC:
465
AN:
5186
South Asian (SAS)
AF:
AC:
324
AN:
4816
European-Finnish (FIN)
AF:
AC:
824
AN:
10600
Middle Eastern (MID)
AF:
AC:
25
AN:
294
European-Non Finnish (NFE)
AF:
AC:
6766
AN:
67994
Other (OTH)
AF:
AC:
213
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
640
1280
1920
2560
3200
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
160
320
480
640
800
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
332
AN:
3478
ClinVar
Significance: association not found
Submissions summary: Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Lip and oral cavity carcinoma Other:1
Nov 02, 2015
Department of Biological Science, Sunandan Divatia School of Science, NMIMS University
Significance:association not found
Review Status:criteria provided, single submitter
Collection Method:case-control
No significant association was observed between SNP rs1435218 with oral cancer. -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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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