rs11802979

Positions:

• chr1-173287195-C-T

Variant summary

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

The XM_047429896.1(TNFSF4):​c.148-80010G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,688 control chromosomes in the GnomAD database, including 7,218 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 0.30 (7218 hom., cov: 31)
• Consequence: TNFSF4 XM_047429896.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351

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]

LOC100506023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNFSF4	XM_047429896.1	c.148-80010G>A		intron_variant			XP_047285852.1
TNFSF4	XM_047429902.1	c.19-80010G>A		intron_variant			XP_047285858.1
LOC100506023	NR_037845.1	n.656-47172G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.297 AC: 44977 AN: 151572 Hom.: 7213 Cov.: 31

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.297 AC: 45008 AN: 151688 Hom.: 7218 Cov.: 31 AF XY: 0.298 AC XY: 22105 AN XY: 74090

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.313

Alfa AF: 0.323 Hom.: 1688

Bravo AF: 0.300

Asia WGS AF: 0.280 AC: 974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11802979; hg19: chr1-173256334;