rs2857708

Variant summary

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

The XM_047418773.1(LTA):​c.-342+4560C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,114 control chromosomes in the GnomAD database, including 959 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 0.10 ( 959 hom., cov: 31)

Consequence

LTA
XM_047418773.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.406
Variant links:
Genes affected
LTA (HGNC:6709): (lymphotoxin alpha) The encoded protein, a member of the tumor necrosis factor family, is a cytokine produced by lymphocytes. The protein is highly inducible, secreted, and forms heterotrimers with lymphotoxin-beta which anchor lymphotoxin-alpha to the cell surface. This protein also mediates a large variety of inflammatory, immunostimulatory, and antiviral responses, is involved in the formation of secondary lymphoid organs during development and plays a role in apoptosis. Genetic variations in this gene are associated with susceptibility to leprosy type 4, myocardial infarction, non-Hodgkin's lymphoma, and psoriatic arthritis. Alternatively spliced transcript variants have been observed for this gene. [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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LTAXM_047418773.1 linkuse as main transcriptc.-342+4560C>T intron_variant XP_047274729.1
LOC100287329NR_149045.1 linkuse as main transcriptn.122-5107G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000289406ENST00000691266.1 linkuse as main transcriptn.119-5107G>A intron_variant

Frequencies

GnomAD3 genomes
AF:
0.104
AC:
15835
AN:
151996
Hom.:
961
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0516
Gnomad AMI
AF:
0.0208
Gnomad AMR
AF:
0.104
Gnomad ASJ
AF:
0.123
Gnomad EAS
AF:
0.123
Gnomad SAS
AF:
0.0826
Gnomad FIN
AF:
0.137
Gnomad MID
AF:
0.0949
Gnomad NFE
AF:
0.131
Gnomad OTH
AF:
0.115
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.104
AC:
15837
AN:
152114
Hom.:
959
Cov.:
31
AF XY:
0.103
AC XY:
7695
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.0515
Gnomad4 AMR
AF:
0.104
Gnomad4 ASJ
AF:
0.123
Gnomad4 EAS
AF:
0.123
Gnomad4 SAS
AF:
0.0825
Gnomad4 FIN
AF:
0.137
Gnomad4 NFE
AF:
0.131
Gnomad4 OTH
AF:
0.114
Alfa
AF:
0.127
Hom.:
1210
Bravo
AF:
0.101
Asia WGS
AF:
0.104
AC:
362
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.8
DANN
Benign
0.65

Splicing

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: rs2857708; hg19: chr6-31533606; API