rs2103867

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014452.5(TNFRSF21):​c.96+10456T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.941 in 152,284 control chromosomes in the GnomAD database, including 67,525 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 0.94 ( 67525 hom., cov: 32)

Consequence

TNFRSF21
NM_014452.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.871
Variant links:
Genes affected
TNFRSF21 (HGNC:13469): (TNF receptor superfamily member 21) This gene encodes a member of the tumor necrosis factor receptor superfamily. The encoded protein activates nuclear factor kappa-B and mitogen-activated protein kinase 8 (also called c-Jun N-terminal kinase 1), and induces cell apoptosis. Through its death domain, the encoded receptor interacts with tumor necrosis factor receptor type 1-associated death domain (TRADD) protein, which is known to mediate signal transduction of tumor necrosis factor receptors. Knockout studies in mice suggest that this gene plays a role in T-helper cell activation, and may be involved in inflammation and immune regulation. [provided by RefSeq, Jul 2013]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TNFRSF21NM_014452.5 linkuse as main transcriptc.96+10456T>G intron_variant ENST00000296861.2 NP_055267.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TNFRSF21ENST00000296861.2 linkuse as main transcriptc.96+10456T>G intron_variant 1 NM_014452.5 ENSP00000296861 P1

Frequencies

GnomAD3 genomes
AF:
0.941
AC:
143169
AN:
152166
Hom.:
67464
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.985
Gnomad AMI
AF:
0.768
Gnomad AMR
AF:
0.938
Gnomad ASJ
AF:
0.919
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.966
Gnomad FIN
AF:
0.940
Gnomad MID
AF:
0.956
Gnomad NFE
AF:
0.912
Gnomad OTH
AF:
0.924
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.941
AC:
143290
AN:
152284
Hom.:
67525
Cov.:
32
AF XY:
0.943
AC XY:
70232
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.985
Gnomad4 AMR
AF:
0.938
Gnomad4 ASJ
AF:
0.919
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.966
Gnomad4 FIN
AF:
0.940
Gnomad4 NFE
AF:
0.912
Gnomad4 OTH
AF:
0.925
Alfa
AF:
0.920
Hom.:
40581
Bravo
AF:
0.942
Asia WGS
AF:
0.984
AC:
3421
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.073
DANN
Benign
0.32

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2103867; hg19: chr6-47266696; API