chr4-53535732-C-T

Variant summary

Our verdict is Benign. Variant got -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

Scores

2

Clinical Significance

association not found criteria provided, single submitter O:1

Conservation

PhyloP100: -0.274
Variant links:
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]
LNX1-AS1 (HGNC:40345): (LNX1 antisense RNA 1)

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=-0.85).
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/exons MANE UniProt
LNX1NM_001126328.3 linkuse as main transcriptc.381-27505G>A intron_variant ENST00000263925.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LNX1ENST00000263925.8 linkuse as main transcriptc.381-27505G>A intron_variant 1 NM_001126328.3 P1Q8TBB1-1
LNX1ENST00000306888.6 linkuse as main transcriptc.92+22142G>A intron_variant 1 Q8TBB1-2
LNX1-AS1ENST00000511989.5 linkuse as main transcriptn.266+11385C>T intron_variant, non_coding_transcript_variant 2
LNX1-AS1ENST00000514364.1 linkuse as main transcriptn.240-3361C>T intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0888
AC:
13507
AN:
152118
Hom.:
580
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0874
Gnomad AMI
AF:
0.0351
Gnomad AMR
AF:
0.0652
Gnomad ASJ
AF:
0.0726
Gnomad EAS
AF:
0.0895
Gnomad SAS
AF:
0.0658
Gnomad FIN
AF:
0.0777
Gnomad MID
AF:
0.0854
Gnomad NFE
AF:
0.0995
Gnomad OTH
AF:
0.0986
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0888
AC:
13524
AN:
152236
Hom.:
583
Cov.:
32
AF XY:
0.0857
AC XY:
6380
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.0873
Gnomad4 AMR
AF:
0.0650
Gnomad4 ASJ
AF:
0.0726
Gnomad4 EAS
AF:
0.0897
Gnomad4 SAS
AF:
0.0673
Gnomad4 FIN
AF:
0.0777
Gnomad4 NFE
AF:
0.0995
Gnomad4 OTH
AF:
0.101
Alfa
AF:
0.0934
Hom.:
361
Bravo
AF:
0.0883
Asia WGS
AF:
0.0950
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
association not found, criteria provided, single submittercase-controlDepartment of Biological Science, Sunandan Divatia School of Science, NMIMS UniversityNov 02, 2015No significant association was observed between SNP rs1435218 with oral cancer. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
2.8
DANN
Benign
0.48

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: rs1435218; hg19: chr4-54401899; API