rs10912564

chr1-173201479-C-T

Variant summary

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

The NM_003326.5(TNFSF4):c.153+5545G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 151,922 control chromosomes in the GnomAD database, including 15,356 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 0.42 (15356 hom., cov: 32)
• Consequence: TNFSF4 NM_003326.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFSF4	NM_003326.5	c.153+5545G>A		intron_variant		ENST00000281834.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFSF4	ENST00000281834.4	c.153+5545G>A		intron_variant		1	NM_003326.5	P1
TNFSF4	ENST00000367718.5	c.3+3832G>A		intron_variant		1
TNFSF4	ENST00000488053.1	n.414+3832G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63442 AN: 151804 Hom.: 15328 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.0955

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.418 AC: 63507 AN: 151922 Hom.: 15356 Cov.: 32 AF XY: 0.416 AC XY: 30902 AN XY: 74242

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.0957

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.414

Alfa AF: 0.349 Hom.: 6923

Bravo AF: 0.435

Asia WGS AF: 0.215 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.29
Dann	Benign	0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10912564; hg19: chr1-173170618;