rs1342032

Variant names:

• chr1-173301510-A-C
• rs1342032
• ENST00000714430.1:c.-126-61487T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-173301510-A-C
• chr1-173301510-A-G
• chr1-173301510-A-T

Variant summary

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

The ENST00000714430.1(TNFSF4):​c.-126-61487T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,662 control chromosomes in the GnomAD database, including 24,595 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 0.57 (24595 hom., cov: 32)
• Consequence: TNFSF4 ENST00000714430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100506023	NR_037845.1	n.656-61487T>G		intron_variant	Intron 2 of 2
TNFSF4	XM_047429896.1	c.148-94325T>G		intron_variant	Intron 2 of 4		XP_047285852.1
TNFSF4	XM_047429902.1	c.19-94325T>G		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.-126-61487T>G		intron_variant	Intron 3 of 6			ENSP00000519699.1
TNFSF4	ENST00000714470.1	c.-127+30169T>G		intron_variant	Intron 3 of 6			ENSP00000519727.1
TNFSF4	ENST00000714471.1	c.-9-94325T>G		intron_variant	Intron 3 of 5			ENSP00000519728.1

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85642 AN: 151542 Hom.: 24577 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.565 AC: 85695 AN: 151662 Hom.: 24595 Cov.: 32 AF XY: 0.563 AC XY: 41749 AN XY: 74142

African (AFR) AF: 0.460 AC: 19053 AN: 41386

American (AMR) AF: 0.571 AC: 8687 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2172 AN: 3456

East Asian (EAS) AF: 0.641 AC: 3286 AN: 5126

South Asian (SAS) AF: 0.640 AC: 3084 AN: 4822

European-Finnish (FIN) AF: 0.565 AC: 5955 AN: 10548

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41451 AN: 67792

Other (OTH) AF: 0.583 AC: 1230 AN: 2110

Alfa AF: 0.600 Hom.: 113980

Bravo AF: 0.560

Asia WGS AF: 0.627 AC: 2182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.50
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1342032; hg19: chr1-173270649;