rs13215091

Variant names:

• chr6-31560913-G-A
• rs13215091
• XM_047418773.1:c.-698G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047418773.1(LTA):​c.-698G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0429 in 152,206 control chromosomes in the GnomAD database, including 246 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 0.043 (246 hom., cov: 32)
• Consequence: LTA XM_047418773.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445
• Publications: 7 publications found

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]

ENSG00000289406 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LTA	XM_047418773.1	c.-698G>A		5_prime_UTR_variant	Exon 1 of 6		XP_047274729.1
LOC100287329	NR_149045.1	n.122-191C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289406	ENST00000691266.2	n.200-191C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0428 AC: 6515 AN: 152088 Hom.: 246 Cov.: 32

Gnomad AFR AF: 0.0170

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.0949

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0759

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0416

Gnomad OTH AF: 0.0403

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0429 AC: 6525 AN: 152206 Hom.: 246 Cov.: 32 AF XY: 0.0475 AC XY: 3532 AN XY: 74422

African (AFR) AF: 0.0171 AC: 710 AN: 41540

American (AMR) AF: 0.0341 AC: 521 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0828 AC: 287 AN: 3468

East Asian (EAS) AF: 0.0947 AC: 490 AN: 5174

South Asian (SAS) AF: 0.157 AC: 756 AN: 4824

European-Finnish (FIN) AF: 0.0759 AC: 804 AN: 10586

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0415 AC: 2825 AN: 68012

Other (OTH) AF: 0.0413 AC: 87 AN: 2108

Alfa AF: 0.0412 Hom.: 305

Bravo AF: 0.0351

Asia WGS AF: 0.106 AC: 369 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	0.081
DANN	Benign	0.39
PhyloP100		-0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13215091; hg19: chr6-31528690;