rs4647191

Variant names:

• chr6-31570861-G-A
• rs4647191
• XM_047418773.1:c.-341-631G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XM_047418773.1(LTA):​c.-341-631G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00899 in 152,156 control chromosomes in the GnomAD database, including 6 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 0.0090 (6 hom., cov: 31)
• Consequence: LTA XM_047418773.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.738

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00899 (1368/152156) while in subpopulation SAS AF= 0.0312 (150/4814). AF 95% confidence interval is 0.0271. There are 6 homozygotes in gnomad4. There are 707 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LTA	XM_047418773.1	c.-341-631G>A		intron_variant	Intron 1 of 5		XP_047274729.1
LOC100287329	NR_149045.1	n.121+1722C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289406	ENST00000691266.1	n.118+1722C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.00898 AC: 1366 AN: 152038 Hom.: 6 Cov.: 31

Gnomad AFR AF: 0.00326

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.00728

Gnomad ASJ AF: 0.00750

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.0307

Gnomad FIN AF: 0.00482

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.00766

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

GnomAD4 genome AF: 0.00899 AC: 1368 AN: 152156 Hom.: 6 Cov.: 31 AF XY: 0.00950 AC XY: 707 AN XY: 74392

Gnomad4 AFR AF: 0.00325

Gnomad4 AMR AF: 0.00727

Gnomad4 ASJ AF: 0.00750

Gnomad4 EAS AF: 0.0104

Gnomad4 SAS AF: 0.0312

Gnomad4 FIN AF: 0.00482

Gnomad4 NFE AF: 0.0118

Gnomad4 OTH AF: 0.00758

Alfa AF: 0.0103 Hom.: 4

Bravo AF: 0.00809

Asia WGS AF: 0.0230 AC: 83 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	3.8
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4647191; hg19: chr6-31538638;