rs844642

Positions:

• chr1-173238697-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047429896.1(TNFSF4):​c.148-31512C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 150,576 control chromosomes in the GnomAD database, including 33,772 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 0.64 (33772 hom., cov: 31)
• Consequence: TNFSF4 XM_047429896.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

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]

LOC100506023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNFSF4	XM_047429896.1	c.148-31512C>T		intron_variant			XP_047285852.1
TNFSF4	XM_047429902.1	c.19-31512C>T		intron_variant			XP_047285858.1
LOC100506023	NR_037845.1	n.1982C>T		non_coding_transcript_exon_variant	3/3
		n.173238697G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.644 AC: 96839 AN: 150458 Hom.: 33705 Cov.: 31

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.644 AC: 96966 AN: 150576 Hom.: 33772 Cov.: 31 AF XY: 0.643 AC XY: 47306 AN XY: 73514

Gnomad4 AFR AF: 0.916

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.640

Alfa AF: 0.580 Hom.: 3451

Bravo AF: 0.663

Asia WGS AF: 0.529 AC: 1839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.81
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs844642; hg19: chr1-173207836;