rs947505

Variant names:

• chr1-173332958-A-G
• rs947505
• XM_047429896.1:c.147+108961T>C

Variant summary

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

The XM_047429896.1(TNFSF4):​c.147+108961T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,294 control chromosomes in the GnomAD database, including 50,535 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 0.81 (50535 hom., cov: 34)
• Consequence: TNFSF4 XM_047429896.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFSF4	XM_047429896.1	c.147+108961T>C		intron_variant	Intron 2 of 4		XP_047285852.1
TNFSF4	XM_047429902.1	c.18+69301T>C		intron_variant	Intron 2 of 4		XP_047285858.1
LOC100506023	NR_037845.1	n.656-92935T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123499 AN: 152176 Hom.: 50507 Cov.: 34

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.811 AC: 123577 AN: 152294 Hom.: 50535 Cov.: 34 AF XY: 0.811 AC XY: 60414 AN XY: 74474

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.879

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.851

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.834

Alfa AF: 0.851 Hom.: 68238

Bravo AF: 0.806

Asia WGS AF: 0.799 AC: 2776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs947505; hg19: chr1-173302097;