rs6425201

chr1-173043664-C-T

Variant summary

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

The NM_005092.4(TNFSF18):c.187+275G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 152,132 control chromosomes in the GnomAD database, including 387 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 0.064 (387 hom., cov: 32)
• Consequence: TNFSF18 NM_005092.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

Genes affected

TNFSF18 (HGNC:11932): (TNF superfamily member 18) The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This cytokine is a ligand for receptor TNFRSF18/AITR/GITR. It has been shown to modulate T lymphocyte survival in peripheral tissues. This cytokine is also found to be expressed in endothelial cells, and is thought to be important for interaction between T lymphocytes and endothelial cells. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFSF18	NM_005092.4	c.187+275G>A		intron_variant		ENST00000404377.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFSF18	ENST00000404377.5	c.187+275G>A		intron_variant		1	NM_005092.4	P1
	ENST00000432694.2	n.665+20091C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0637 AC: 9678 AN: 152016 Hom.: 387 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0662

Gnomad ASJ AF: 0.0461

Gnomad EAS AF: 0.0314

Gnomad SAS AF: 0.0895

Gnomad FIN AF: 0.0181

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0637 AC: 9694 AN: 152132 Hom.: 387 Cov.: 32 AF XY: 0.0630 AC XY: 4682 AN XY: 74352

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0661

Gnomad4 ASJ AF: 0.0461

Gnomad4 EAS AF: 0.0311

Gnomad4 SAS AF: 0.0886

Gnomad4 FIN AF: 0.0181

Gnomad4 NFE AF: 0.0401

Gnomad4 OTH AF: 0.0672

Alfa AF: 0.0482 Hom.: 300

Bravo AF: 0.0682

Asia WGS AF: 0.0750 AC: 260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	2.9
Dann	Benign	0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6425201; hg19: chr1-173012804;