rs975074

Variant names:

• chr1-173044627-C-A
• rs975074
• NM_005092.4:c.157-658G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-173044627-C-A
• chr1-173044627-C-G
• chr1-173044627-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005092.4(TNFSF18):​c.157-658G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 152,122 control chromosomes in the GnomAD database, including 25,609 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 0.57 (25609 hom., cov: 33)
• Consequence: TNFSF18 NM_005092.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421
• Publications: 7 publications found

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]

ENSG00000224000 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005092.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFSF18	NM_005092.4	MANE Select	c.157-658G>T		intron	N/A	NP_005083.3	Q9UNG2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFSF18	ENST00000404377.5	TSL:1 MANE Select	c.157-658G>T		intron	N/A	ENSP00000385470.4	Q9UNG2
	ENSG00000224000	ENST00000432694.2	TSL:3	n.666-19246C>A		intron	N/A
	ENSG00000224000	ENST00000717048.1		n.324-19246C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87124 AN: 152004 Hom.: 25569 Cov.: 33

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.573 AC: 87223 AN: 152122 Hom.: 25609 Cov.: 33 AF XY: 0.579 AC XY: 43013 AN XY: 74352

African (AFR) AF: 0.570 AC: 23661 AN: 41502

American (AMR) AF: 0.619 AC: 9456 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2177 AN: 3472

East Asian (EAS) AF: 0.913 AC: 4720 AN: 5172

South Asian (SAS) AF: 0.757 AC: 3653 AN: 4828

European-Finnish (FIN) AF: 0.518 AC: 5481 AN: 10590

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36074 AN: 67964

Other (OTH) AF: 0.595 AC: 1258 AN: 2116

Alfa AF: 0.549 Hom.: 60403

Bravo AF: 0.578

Asia WGS AF: 0.832 AC: 2889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.31
PhyloP100		0.42
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs975074; hg19: chr1-173013767;