chr1-173263668-A-T

Variant names:

• chr1-173263668-A-T
• rs844654
• XM_047429896.1:c.148-56483T>A

Variant summary

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

The XM_047429896.1(TNFSF4):​c.148-56483T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 152,022 control chromosomes in the GnomAD database, including 16,347 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 0.46 (16347 hom., cov: 32)
• Consequence: TNFSF4 XM_047429896.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

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 (AMR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFSF4	XM_047429896.1	c.148-56483T>A		intron_variant	Intron 2 of 4		XP_047285852.1
TNFSF4	XM_047429902.1	c.19-56483T>A		intron_variant	Intron 2 of 4		XP_047285858.1
LOC100506023	NR_037845.1	n.656-23645T>A		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69773 AN: 151904 Hom.: 16318 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.459 AC: 69842 AN: 152022 Hom.: 16347 Cov.: 32 AF XY: 0.460 AC XY: 34196 AN XY: 74306

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.460

Alfa AF: 0.442 Hom.: 1841

Bravo AF: 0.473

Asia WGS AF: 0.440 AC: 1530 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	0.93
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs844654; hg19: chr1-173232807;