rs723858

Positions:

• chr1-173049123-T-A
• chr1-173049123-T-C
• chr1-173049123-T-G

Variant summary

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

The NM_005092.4(TNFSF18):​c.156+1618A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,094 control chromosomes in the GnomAD database, including 4,785 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 0.20 (4785 hom., cov: 32)
• Consequence: TNFSF18 NM_005092.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFSF18	NM_005092.4	c.156+1618A>T		intron_variant		ENST00000404377.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFSF18	ENST00000404377.5	c.156+1618A>T		intron_variant		1	NM_005092.4	P1
	ENST00000432694.2	n.666-14750T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30880 AN: 151976 Hom.: 4794 Cov.: 32

Gnomad AFR AF: 0.0516

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.203 AC: 30871 AN: 152094 Hom.: 4785 Cov.: 32 AF XY: 0.210 AC XY: 15605 AN XY: 74334

Gnomad4 AFR AF: 0.0514

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.242

Alfa AF: 0.188 Hom.: 394

Bravo AF: 0.208

Asia WGS AF: 0.532 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.56
DANN	Benign	0.47

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: rs723858; hg19: chr1-173018263;