rs4916363

Variant names:

• chr1-173472929-G-A
• rs4916363
• ENST00000714430.1:c.-359+3703C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-173472929-G-A
• chr1-173472929-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000714430.1(TNFSF4):​c.-359+3703C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,946 control chromosomes in the GnomAD database, including 29,649 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 0.60 (29649 hom., cov: 31)
• Consequence: TNFSF4 ENST00000714430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 2 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]

PRDX6-AS1 (HGNC:54870): (PRDX6 antisense RNA 1)

LOC100506023 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000714430.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC100506023	NR_037845.1		n.524+3703C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFSF4	ENST00000714430.1		c.-359+3703C>T		intron	N/A	ENSP00000519699.1
	TNFSF4	ENST00000714470.1		c.-342+3703C>T		intron	N/A	ENSP00000519727.1
	TNFSF4	ENST00000714471.1		c.-309+3703C>T		intron	N/A	ENSP00000519728.1

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90982 AN: 151828 Hom.: 29661 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.599 AC: 90973 AN: 151946 Hom.: 29649 Cov.: 31 AF XY: 0.603 AC XY: 44784 AN XY: 74258

African (AFR) AF: 0.331 AC: 13706 AN: 41414

American (AMR) AF: 0.714 AC: 10896 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2230 AN: 3472

East Asian (EAS) AF: 0.406 AC: 2095 AN: 5166

South Asian (SAS) AF: 0.779 AC: 3754 AN: 4822

European-Finnish (FIN) AF: 0.721 AC: 7611 AN: 10554

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48475 AN: 67938

Other (OTH) AF: 0.644 AC: 1357 AN: 2106

Alfa AF: 0.644 Hom.: 4128

Bravo AF: 0.582

Asia WGS AF: 0.557 AC: 1939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.79
DANN	Benign	0.38
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs4916363; hg19: chr1-173442068;