Variant chr17-16939133-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.*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

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]

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 17-16939133-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
TNFRSF13B	NM_012452.3 linkuse as main transcript	c.*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
TNFRSF13B	ENST00000261652.7 linkuse as main transcript	c.*414G>A		3_prime_UTR_variant	5/5	1	NM_012452.3	ENSP00000261652	P2	O14836-1

Frequencies

GnomAD3 genomes

AF:

0.0848

AC:

12888

AN:

151966

Hom.:

874

Cov.:

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.:

Cov.:

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.:

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 submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough 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.

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