rs1342032

Positions:

• chr1-173301510-A-C
• chr1-173301510-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047429896.1(TNFSF4):​c.148-94325T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,662 control chromosomes in the GnomAD database, including 24,595 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 0.57 (24595 hom., cov: 32)
• Consequence: TNFSF4 XM_047429896.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248

Genes affected

TNFSF4 (HGNC:11934): (TNF superfamily member 4) This gene encodes a cytokine of the tumor necrosis factor (TNF) ligand family. The encoded protein functions in T cell antigen-presenting cell (APC) interactions and mediates adhesion of activated T cells to endothelial cells. Polymorphisms in this gene have been associated with Sjogren's syndrome and systemic lupus erythematosus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNFSF4	XM_047429896.1	c.148-94325T>G		intron_variant			XP_047285852.1
TNFSF4	XM_047429902.1	c.19-94325T>G		intron_variant			XP_047285858.1
		n.173301510A>C		intergenic_region
LOC100506023	NR_037845.1	n.656-61487T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85642 AN: 151542 Hom.: 24577 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.565 AC: 85695 AN: 151662 Hom.: 24595 Cov.: 32 AF XY: 0.563 AC XY: 41749 AN XY: 74142

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.583

Alfa AF: 0.607 Hom.: 54378

Bravo AF: 0.560

Asia WGS AF: 0.627 AC: 2182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1342032; hg19: chr1-173270649;