17-16939133-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_012452.3(TNFRSF13B):​c.*414G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0828 in 166,062 control chromosomes in the GnomAD database, including 922 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.085 ( 871 hom., cov: 31)
Exomes 𝑓: 0.062 ( 51 hom. )

Consequence

TNFRSF13B
NM_012452.3 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.63
Variant links:
Genes affected
TNFRSF13B (HGNC:18153): (TNF receptor superfamily member 13B) The protein encoded by this gene is a lymphocyte-specific member of the tumor necrosis factor (TNF) receptor superfamily. It interacts with calcium-modulator and cyclophilin ligand (CAML). The protein induces activation of the transcription factors NFAT, AP1, and NF-kappa-B and plays a crucial role in humoral immunity by interacting with a TNF ligand. This gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
Variant 17-16939133-C-T is Benign according to our data. Variant chr17-16939133-C-T is described in ClinVar as [Benign]. Clinvar id is 322018.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TNFRSF13BNM_012452.3 linkuse as main transcriptc.*414G>A 3_prime_UTR_variant 5/5 ENST00000261652.7 NP_036584.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TNFRSF13BENST00000261652.7 linkuse as main transcriptc.*414G>A 3_prime_UTR_variant 5/51 NM_012452.3 ENSP00000261652 P2O14836-1

Frequencies

GnomAD3 genomes
AF:
0.0848
AC:
12888
AN:
151966
Hom.:
874
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0841
Gnomad AMI
AF:
0.0702
Gnomad AMR
AF:
0.0945
Gnomad ASJ
AF:
0.0484
Gnomad EAS
AF:
0.409
Gnomad SAS
AF:
0.136
Gnomad FIN
AF:
0.0727
Gnomad MID
AF:
0.0633
Gnomad NFE
AF:
0.0594
Gnomad OTH
AF:
0.0722
GnomAD4 exome
AF:
0.0620
AC:
866
AN:
13978
Hom.:
51
Cov.:
0
AF XY:
0.0638
AC XY:
448
AN XY:
7024
show subpopulations
Gnomad4 AFR exome
AF:
0.0598
Gnomad4 AMR exome
AF:
0.0438
Gnomad4 ASJ exome
AF:
0.0311
Gnomad4 EAS exome
AF:
0.330
Gnomad4 SAS exome
AF:
0.0921
Gnomad4 FIN exome
AF:
0.0448
Gnomad4 NFE exome
AF:
0.0481
Gnomad4 OTH exome
AF:
0.0659
GnomAD4 genome
AF:
0.0847
AC:
12887
AN:
152084
Hom.:
871
Cov.:
31
AF XY:
0.0891
AC XY:
6621
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.0839
Gnomad4 AMR
AF:
0.0946
Gnomad4 ASJ
AF:
0.0484
Gnomad4 EAS
AF:
0.409
Gnomad4 SAS
AF:
0.135
Gnomad4 FIN
AF:
0.0727
Gnomad4 NFE
AF:
0.0593
Gnomad4 OTH
AF:
0.0714
Alfa
AF:
0.0644
Hom.:
111
Bravo
AF:
0.0850
Asia WGS
AF:
0.249
AC:
863
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Common Variable Immune Deficiency, Dominant Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.12
DANN
Benign
0.42

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: rs55701306; hg19: chr17-16842447; API