ENST00000714430.1:c.-127+77995T>C

Variant names:

• chr1-173345879-A-G
• rs7550607
• ENST00000714430.1:c.-127+77995T>C

Variant summary

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

The ENST00000714430.1(TNFSF4):​c.-127+77995T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0984 in 152,204 control chromosomes in the GnomAD database, including 865 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 0.098 (865 hom., cov: 31)
• Consequence: TNFSF4 ENST00000714430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 4 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

LOC100506023 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100506023	NR_037845.1	n.656-105856T>C		intron_variant	Intron 2 of 2
TNFSF4	XM_047429896.1	c.147+96040T>C		intron_variant	Intron 2 of 4		XP_047285852.1
TNFSF4	XM_047429902.1	c.18+56380T>C		intron_variant	Intron 2 of 4		XP_047285858.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFSF4	ENST00000714430.1	c.-127+77995T>C		intron_variant	Intron 3 of 6			ENSP00000519699.1
TNFSF4	ENST00000714470.1	c.-210-14117T>C		intron_variant	Intron 2 of 6			ENSP00000519727.1
TNFSF4	ENST00000714471.1	c.-10+115314T>C		intron_variant	Intron 3 of 5			ENSP00000519728.1

Frequencies

GnomAD3 genomes AF: 0.0982 AC: 14933 AN: 152086 Hom.: 860 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0771

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0871

Gnomad OTH AF: 0.0709

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

GnomAD4 genome AF: 0.0984 AC: 14981 AN: 152204 Hom.: 865 Cov.: 31 AF XY: 0.101 AC XY: 7483 AN XY: 74420

African (AFR) AF: 0.101 AC: 4198 AN: 41534

American (AMR) AF: 0.0772 AC: 1182 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0476 AC: 165 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1389 AN: 5172

South Asian (SAS) AF: 0.134 AC: 646 AN: 4824

European-Finnish (FIN) AF: 0.120 AC: 1274 AN: 10610

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0871 AC: 5919 AN: 67972

Other (OTH) AF: 0.0758 AC: 160 AN: 2110

Alfa AF: 0.0922 Hom.: 613

Bravo AF: 0.0957

Asia WGS AF: 0.223 AC: 774 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	0.032
DANN	Benign	0.24
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs7550607; hg19: chr1-173315018;