rs35152701

Variant names:

• chr1-173475507-G-A
• rs35152701
• ENST00000714430.1:c.-359+1125C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000714430.1(TNFSF4):​c.-359+1125C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0212 in 152,290 control chromosomes in the GnomAD database, including 44 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 0.021 (44 hom., cov: 34)
• Consequence: TNFSF4 ENST00000714430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• 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]

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=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0212 (3223/152290) while in subpopulation NFE AF = 0.0327 (2225/68006). AF 95% confidence interval is 0.0316. There are 44 homozygotes in GnomAd4. There are 1555 alleles in the male GnomAd4 subpopulation. Median coverage is 34. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 44 Unknown gene

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+1125C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFSF4	ENST00000714430.1		c.-359+1125C>T		intron	N/A	ENSP00000519699.1
	TNFSF4	ENST00000714470.1		c.-342+1125C>T		intron	N/A	ENSP00000519727.1
	TNFSF4	ENST00000714471.1		c.-309+1125C>T		intron	N/A	ENSP00000519728.1

Frequencies

GnomAD3 genomes AF: 0.0212 AC: 3220 AN: 152172 Hom.: 44 Cov.: 34

Gnomad AFR AF: 0.00635

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0185

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.0228

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0327

Gnomad OTH AF: 0.0143

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

GnomAD4 genome AF: 0.0212 AC: 3223 AN: 152290 Hom.: 44 Cov.: 34 AF XY: 0.0209 AC XY: 1555 AN XY: 74482

African (AFR) AF: 0.00633 AC: 263 AN: 41568

American (AMR) AF: 0.0185 AC: 283 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3470

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.0116 AC: 56 AN: 4832

European-Finnish (FIN) AF: 0.0228 AC: 242 AN: 10602

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0327 AC: 2225 AN: 68006

Other (OTH) AF: 0.0142 AC: 30 AN: 2114

Alfa AF: 0.0204 Hom.: 26

Bravo AF: 0.0190

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.20
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs35152701; hg19: chr1-173444646;