Variant chr16-11967817-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001192.3(TNFRSF17):c.525G>A(p.Thr175=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0413 in 1,613,968 control chromosomes in the GnomAD database, including 2,728 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 0.052 ( 334 hom., cov: 32)

Exomes 𝑓: 0.040 ( 2394 hom. )

Consequence

TNFRSF17
NM_001192.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.363

Variant links:

Genes affected

TNFRSF17 (HGNC:11913): (TNF receptor superfamily member 17) The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor is preferentially expressed in mature B lymphocytes, and may be important for B cell development and autoimmune response. This receptor has been shown to specifically bind to the tumor necrosis factor (ligand) superfamily, member 13b (TNFSF13B/TALL-1/BAFF), and to lead to NF-kappaB and MAPK8/JNK activation. This receptor also binds to various TRAF family members, and thus may transduce signals for cell survival and proliferation. [provided by RefSeq, Jul 2008]

TNFRSF17 links:

NPIPB2 (HGNC:37451): (nuclear pore complex interacting protein family member B2) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

NPIPB2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP7

Synonymous conserved (PhyloP=-0.363 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFRSF17	NM_001192.3 linkuse as main transcript	c.525G>A	p.Thr175=	synonymous_variant	3/3	ENST00000053243.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFRSF17	ENST00000053243.6 linkuse as main transcript	c.525G>A	p.Thr175=	synonymous_variant	3/3	1	NM_001192.3	P1	Q02223-1

Frequencies

GnomAD3 genomes

AF:

0.0519

AC:

7895

AN:

152090

Hom.:

331

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0546

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.0829

Gnomad EAS

AF:

0.0693

Gnomad SAS

AF:

0.0166

Gnomad FIN

AF:

0.0368

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0343

Gnomad OTH

AF:

0.0479

GnomAD3 exomes

AF:

0.0680

AC:

17092

AN:

251210

Hom.:

1403

AF XY:

0.0598

AC XY:

8115

AN XY:

135778

show subpopulations

Gnomad AFR exome

AF:

0.0603

Gnomad AMR exome

AF:

0.242

Gnomad ASJ exome

AF:

0.0744

Gnomad EAS exome

AF:

0.0700

Gnomad SAS exome

AF:

0.0167

Gnomad FIN exome

AF:

0.0402

Gnomad NFE exome

AF:

0.0353

Gnomad OTH exome

AF:

0.0570

GnomAD4 exome

AF:

0.0402

AC:

58825

AN:

1461760

Hom.:

2394

Cov.:

AF XY:

0.0390

AC XY:

28336

AN XY:

727150

show subpopulations

Gnomad4 AFR exome

AF:

0.0575

Gnomad4 AMR exome

AF:

0.229

Gnomad4 ASJ exome

AF:

0.0751

Gnomad4 EAS exome

AF:

0.0882

Gnomad4 SAS exome

AF:

0.0184

Gnomad4 FIN exome

AF:

0.0405

Gnomad4 NFE exome

AF:

0.0313

Gnomad4 OTH exome

AF:

0.0411

GnomAD4 genome

AF:

0.0519

AC:

7900

AN:

152208

Hom.:

334

Cov.:

AF XY:

0.0531

AC XY:

3948

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.0545

Gnomad4 AMR

AF:

0.134

Gnomad4 ASJ

AF:

0.0829

Gnomad4 EAS

AF:

0.0694

Gnomad4 SAS

AF:

0.0166

Gnomad4 FIN

AF:

0.0368

Gnomad4 NFE

AF:

0.0343

Gnomad4 OTH

AF:

0.0474

Alfa

AF:

0.0468

Hom.:

254

Bravo

AF:

0.0643

Asia WGS

AF:

0.0500

AC:

175

AN:

3478

EpiCase

AF:

0.0321

EpiControl

AF:

0.0329

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

1.8

DANN

Benign

0.90

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over