rs1886204

Variant summary

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

The NM_153371.4(LNX2):​c.-100-18401C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,960 control chromosomes in the GnomAD database, including 10,861 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 0.36 ( 10861 hom., cov: 32)

Consequence

LNX2
NM_153371.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.787
Variant links:
Genes affected
LNX2 (HGNC:20421): (ligand of numb-protein X 2) Predicted to enable ubiquitin-protein transferase activity. Predicted to be involved in protein ubiquitination. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.54).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LNX2NM_153371.4 linkuse as main transcriptc.-100-18401C>T intron_variant ENST00000316334.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LNX2ENST00000316334.5 linkuse as main transcriptc.-100-18401C>T intron_variant 1 NM_153371.4 P1
LNX2ENST00000649248.1 linkuse as main transcriptc.-101+6526C>T intron_variant P1

Frequencies

GnomAD3 genomes
AF:
0.365
AC:
55374
AN:
151842
Hom.:
10856
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.511
Gnomad AMI
AF:
0.317
Gnomad AMR
AF:
0.317
Gnomad ASJ
AF:
0.364
Gnomad EAS
AF:
0.350
Gnomad SAS
AF:
0.317
Gnomad FIN
AF:
0.273
Gnomad MID
AF:
0.421
Gnomad NFE
AF:
0.306
Gnomad OTH
AF:
0.360
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.365
AC:
55419
AN:
151960
Hom.:
10861
Cov.:
32
AF XY:
0.361
AC XY:
26798
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.511
Gnomad4 AMR
AF:
0.317
Gnomad4 ASJ
AF:
0.364
Gnomad4 EAS
AF:
0.350
Gnomad4 SAS
AF:
0.318
Gnomad4 FIN
AF:
0.273
Gnomad4 NFE
AF:
0.306
Gnomad4 OTH
AF:
0.360
Alfa
AF:
0.222
Hom.:
551
Bravo
AF:
0.375
Asia WGS
AF:
0.296
AC:
1029
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
0.58
DANN
Benign
0.36

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: rs1886204; hg19: chr13-28174341; API