chr1-2556705-CCACCCCCAAAACCGACGTCT-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_003820.4(TNFRSF14):​c.42_61delCACCCCCAAAACCGACGTCT​(p.Thr15GlufsTer55) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as other (no stars).

Frequency

Genomes: not found (cov: 33)

Consequence

TNFRSF14
NM_003820.4 frameshift

Scores

Not classified

Clinical Significance

- - O:1

Conservation

PhyloP100: -0.0480
Variant links:
Genes affected
TNFRSF14 (HGNC:11912): (TNF receptor superfamily member 14) This gene encodes a member of the TNF (tumor necrosis factor) receptor superfamily. The encoded protein functions in signal transduction pathways that activate inflammatory and inhibitory T-cell immune response. It binds herpes simplex virus (HSV) viral envelope glycoprotein D (gD), mediating its entry into cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
TNFRSF14-AS1 (HGNC:26966): (TNFRSF14 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TNFRSF14NM_003820.4 linkc.42_61delCACCCCCAAAACCGACGTCT p.Thr15GlufsTer55 frameshift_variant Exon 1 of 8 ENST00000355716.5 NP_003811.2 Q92956-1A0A024R052

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TNFRSF14ENST00000355716.5 linkc.42_61delCACCCCCAAAACCGACGTCT p.Thr15GlufsTer55 frameshift_variant Exon 1 of 8 1 NM_003820.4 ENSP00000347948.4 Q92956-1

Frequencies

GnomAD3 genomes
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
33

ClinVar

Significance: -
Submissions summary: Other:1
Revision: -
LINK: link

Submissions by phenotype

Neoplasm Other:1
Mar 04, 2025
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital
Significance: -
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-2488144; API