rs1322058

Positions:

• chr9-114922267-C-T

Variant summary

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

The NM_001244.4(TNFSF8):​c.196-4129G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,962 control chromosomes in the GnomAD database, including 10,504 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 0.36 (10504 hom., cov: 32)
• Consequence: TNFSF8 NM_001244.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

Genes affected

TNFSF8 (HGNC:11938): (TNF superfamily member 8) 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 TNFRSF8/CD30, which is a cell surface antigen and a marker for Hodgkin lymphoma and related hematologic malignancies. The engagement of this cytokine expressed on B cell surface plays an inhibitory role in modulating Ig class switch. This cytokine was shown to enhance cell proliferation of some lymphoma cell lines, while to induce cell death and reduce cell proliferation of other lymphoma cell lines. The pleiotropic biologic activities of this cytokine on different CD30+ lymphoma cell lines may play a pathophysiologic role in Hodgkin's and some non-Hodgkin's lymphomas. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

DELEC1 (HGNC:23658): (deleted in esophageal cancer 1) The function of this gene is not known. This gene is located in a region commonly deleted in esophageal squamous cell carcinomas. Gene expression is reduced or absent in these carcinomas and thus this is a candidate tumor suppressor gene for esophageal squamous cell carcinomas. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNFSF8	NM_001244.4	c.196-4129G>A		intron_variant		ENST00000223795.3	NP_001235.1
TNFSF8	NM_001252290.1	c.196-4129G>A		intron_variant			NP_001239219.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNFSF8	ENST00000223795.3	c.196-4129G>A		intron_variant		1	NM_001244.4	ENSP00000223795	P1
TNFSF8	ENST00000618336.4	c.196-4129G>A		intron_variant		3		ENSP00000484651
DELEC1	ENST00000648852.1	n.198+669C>T		intron_variant, non_coding_transcript_variant
DELEC1	ENST00000649565.1	n.225+36959C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55178 AN: 151844 Hom.: 10493 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.363 AC: 55216 AN: 151962 Hom.: 10504 Cov.: 32 AF XY: 0.366 AC XY: 27191 AN XY: 74274

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.363

Alfa AF: 0.395 Hom.: 5673

Bravo AF: 0.360

Asia WGS AF: 0.384 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
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: rs1322058; hg19: chr9-117684547;