rs5778749

Variant names:

• chr1-173203284-GC-G
• rs5778749
• NM_003326.5:c.153+3739delG

Your query was ambiguous. Multiple possible variants found:

• chr1-173203284-GC-G
• chr1-173203284-GC-GCC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_003326.5(TNFSF4):​c.153+3739delG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,030 control chromosomes in the GnomAD database, including 1,030 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1030 hom., cov: 31)
• Consequence: TNFSF4 NM_003326.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 1 publications found

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]

TNFSF4 Gene-Disease associations (from GenCC):

• systemic lupus erythematosus

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFSF4	NM_003326.5	c.153+3739delG		intron_variant	Intron 1 of 2	ENST00000281834.4	NP_003317.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFSF4	ENST00000281834.4	c.153+3739delG		intron_variant	Intron 1 of 2	1	NM_003326.5	ENSP00000281834.3

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16284 AN: 151912 Hom.: 1029 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0531

Gnomad FIN AF: 0.0690

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0781

Gnomad OTH AF: 0.0986

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

GnomAD4 genome AF: 0.107 AC: 16297 AN: 152030 Hom.: 1030 Cov.: 31 AF XY: 0.109 AC XY: 8093 AN XY: 74330

African (AFR) AF: 0.159 AC: 6606 AN: 41450

American (AMR) AF: 0.141 AC: 2155 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3470

East Asian (EAS) AF: 0.143 AC: 738 AN: 5164

South Asian (SAS) AF: 0.0523 AC: 252 AN: 4816

European-Finnish (FIN) AF: 0.0690 AC: 729 AN: 10572

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.0781 AC: 5306 AN: 67966

Other (OTH) AF: 0.0990 AC: 209 AN: 2112

Alfa AF: 0.100 Hom.: 100

Bravo AF: 0.114

Asia WGS AF: 0.0970 AC: 337 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.22
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5778749; hg19: chr1-173172423;