Variant 17-16939374-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_012452.3(TNFRSF13B):c.*173G>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 0.358 in 738,034 control chromosomes in the GnomAD database, including 49,862 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.39 ( 11763 hom., cov: 28)

Exomes 𝑓: 0.35 ( 38099 hom. )

Consequence

TNFRSF13B
NM_012452.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.56

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]

TNFRSF13B links:

TNFRSF13B (HGNC:):

TNFRSF13B links:

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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 17-16939374-C-T is Benign according to our data. Variant chr17-16939374-C-T is described in ClinVar as [Benign]. Clinvar id is 322022.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNFRSF13B	NM_012452.3 linkuse as main transcript	c.*173G>A		3_prime_UTR_variant	5/5	ENST00000261652.7	NP_036584.1	O14836-1Q4ACX1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNFRSF13B	ENST00000261652 linkuse as main transcript	c.*173G>A		3_prime_UTR_variant	5/5	1	NM_012452.3	ENSP00000261652.2		O14836-1

Frequencies

GnomAD3 genomes

AF:

0.390

AC:

58707

AN:

150492

Hom.:

11741

Cov.:

show subpopulations

Gnomad AFR

AF:

0.474

Gnomad AMI

AF:

0.328

Gnomad AMR

AF:

0.412

Gnomad ASJ

AF:

0.400

Gnomad EAS

AF:

0.536

Gnomad SAS

AF:

0.386

Gnomad FIN

AF:

0.293

Gnomad MID

AF:

0.383

Gnomad NFE

AF:

0.340

Gnomad OTH

AF:

0.373

GnomAD4 exome

AF:

0.350

AC:

205332

AN:

587424

Hom.:

38099

Cov.:

AF XY:

0.351

AC XY:

104426

AN XY:

297154

show subpopulations

Gnomad4 AFR exome

AF:

0.473

Gnomad4 AMR exome

AF:

0.390

Gnomad4 ASJ exome

AF:

0.391

Gnomad4 EAS exome

AF:

0.565

Gnomad4 SAS exome

AF:

0.382

Gnomad4 FIN exome

AF:

0.291

Gnomad4 NFE exome

AF:

0.328

Gnomad4 OTH exome

AF:

0.370

GnomAD4 genome

AF:

0.390

AC:

58780

AN:

150610

Hom.:

11763

Cov.:

AF XY:

0.391

AC XY:

28748

AN XY:

73508

show subpopulations

Gnomad4 AFR

AF:

0.474

Gnomad4 AMR

AF:

0.413

Gnomad4 ASJ

AF:

0.400

Gnomad4 EAS

AF:

0.536

Gnomad4 SAS

AF:

0.386

Gnomad4 FIN

AF:

0.293

Gnomad4 NFE

AF:

0.340

Gnomad4 OTH

AF:

0.369

Alfa

AF:

0.369

Hom.:

1388

Bravo

AF:

0.404

Asia WGS

AF:

0.444

AC:

1545

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -

Common Variable Immune Deficiency, Dominant

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.39

DANN

Benign

0.21

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over