Genetic Variant NM_003820.4:c.42_61delCACCCCCAAAACCGACGTCT (chr1-2556705-CCACCCCCAAAACCGACGTCT-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

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. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: not found (cov: 33)

Consequence

TNFRSF14
NM_003820.4 frameshift

Scores

Not classified

Clinical Significance

Other O:1

Conservation

PhyloP100: -0.0480

Publications

0 publications found

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 links:

TNFRSF14-AS1 (HGNC:26966): (TNFRSF14 antisense RNA 1)

TNFRSF14-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003820.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
TNFRSF14	NM_003820.4	MANE Select	c.42_61delCACCCCCAAAACCGACGTCT	p.Thr15GlufsTer55	frameshift	Exon 1 of 8	NP_003811.2
TNFRSF14	NM_001297605.2		c.42_61delCACCCCCAAAACCGACGTCT	p.Thr15GlufsTer55	frameshift	Exon 1 of 7	NP_001284534.1
TNFRSF14-AS1	NR_037844.2		n.36-29_36-10delAGACGTCGGTTTTGGGGGTG		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TNFRSF14	ENST00000355716.5	TSL:1 MANE Select	c.42_61delCACCCCCAAAACCGACGTCT	p.Thr15GlufsTer55	frameshift	Exon 1 of 8	ENSP00000347948.4	Q92956-1
TNFRSF14	ENST00000475523.5	TSL:1	n.70+251_70+270delCACCCCCAAAACCGACGTCT		intron	N/A
TNFRSF14	ENST00000860787.1		c.42_61delCACCCCCAAAACCGACGTCT	p.Thr15GlufsTer55	frameshift	Exon 1 of 8	ENSP00000530846.1

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Other

Revision:

View on ClinVar

Pathogenic

VUS

Benign

Condition

Neoplasm (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.048

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over