Variant rs587777988 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_003820.4(TNFRSF14):c.305-364C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 1,414,678 control chromosomes in the GnomAD database, including 189,792 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.58 ( 26210 hom., cov: 32)

Exomes 𝑓: 0.51 ( 163582 hom. )

Consequence

TNFRSF14
NM_003820.4 intron

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: -0.0550

Variant links:

Genes affected

TNFRSF14 (HGNC:11912): (TNF receptor superfamily member 14) This gene encodes a member of the TNF (tumor necrosis factor) receptor superfamily. The encoded protein functions in signal transduction pathways that activate inflammatory and inhibitory T-cell immune response. It binds herpes simplex virus (HSV) viral envelope glycoprotein D (gD), mediating its entry into cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

TNFRSF14 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNFRSF14	NM_003820.4 linkuse as main transcript	c.305-364C>A		intron_variant		ENST00000355716.5	NP_003811.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNFRSF14	ENST00000355716.5 linkuse as main transcript	c.305-364C>A		intron_variant		1	NM_003820.4	ENSP00000347948	P1	Q92956-1

Frequencies

GnomAD3 genomes

AF:

0.576

AC:

87219

AN:

151398

Hom.:

26162

Cov.:

show subpopulations

Gnomad AFR

AF:

0.755

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.563

Gnomad ASJ

AF:

0.457

Gnomad EAS

AF:

0.539

Gnomad SAS

AF:

0.656

Gnomad FIN

AF:

0.507

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.490

Gnomad OTH

AF:

0.550

GnomAD3 exomes

AF:

0.541

AC:

72790

AN:

134530

Hom.:

20180

AF XY:

0.544

AC XY:

39825

AN XY:

73252

show subpopulations

Gnomad AFR exome

AF:

0.771

Gnomad AMR exome

AF:

0.540

Gnomad ASJ exome

AF:

0.456

Gnomad EAS exome

AF:

0.539

Gnomad SAS exome

AF:

0.654

Gnomad FIN exome

AF:

0.486

Gnomad NFE exome

AF:

0.487

Gnomad OTH exome

AF:

0.518

GnomAD4 exome

AF:

0.509

AC:

642565

AN:

1263168

Hom.:

163582

Cov.:

AF XY:

0.512

AC XY:

317071

AN XY:

618694

show subpopulations

Gnomad4 AFR exome

AF:

0.764

Gnomad4 AMR exome

AF:

0.538

Gnomad4 ASJ exome

AF:

0.463

Gnomad4 EAS exome

AF:

0.521

Gnomad4 SAS exome

AF:

0.642

Gnomad4 FIN exome

AF:

0.484

Gnomad4 NFE exome

AF:

0.490

Gnomad4 OTH exome

AF:

0.526

GnomAD4 genome

AF:

0.576

AC:

87317

AN:

151510

Hom.:

26210

Cov.:

AF XY:

0.578

AC XY:

42775

AN XY:

74054

show subpopulations

Gnomad4 AFR

AF:

0.755

Gnomad4 AMR

AF:

0.562

Gnomad4 ASJ

AF:

0.457

Gnomad4 EAS

AF:

0.537

Gnomad4 SAS

AF:

0.656

Gnomad4 FIN

AF:

0.507

Gnomad4 NFE

AF:

0.489

Gnomad4 OTH

AF:

0.554

Alfa

AF:

0.491

Hom.:

5098

Bravo

AF:

0.580

Asia WGS

AF:

0.678

AC:

2361

AN:

3478

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

LINK: link

Submissions by phenotype

not specified

Other:1

not provided, no classification provided

reference population

ITMI

Sep 19, 2013

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.88

DANN

Benign

0.34

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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