Variant rs587777997 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.305-57C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 1,558,776 control chromosomes in the GnomAD database, including 214,939 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 ( 26835 hom., cov: 33)

Exomes 𝑓: 0.51 ( 188104 hom. )

Consequence

TNFRSF14
NM_003820.4 intron

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: -1.93

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 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.305-57C>T		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.305-57C>T		intron_variant		1	NM_003820.4	ENSP00000347948	P1	Q92956-1

Frequencies

GnomAD3 genomes

AF:

0.580

AC:

88150

AN:

151980

Hom.:

26787

Cov.:

show subpopulations

Gnomad AFR

AF:

0.768

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.564

Gnomad ASJ

AF:

0.458

Gnomad EAS

AF:

0.544

Gnomad SAS

AF:

0.651

Gnomad FIN

AF:

0.510

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.489

Gnomad OTH

AF:

0.548

GnomAD3 exomes

AF:

0.553

AC:

93669

AN:

169440

Hom.:

26473

AF XY:

0.553

AC XY:

50934

AN XY:

92036

show subpopulations

Gnomad AFR exome

AF:

0.797

Gnomad AMR exome

AF:

0.548

Gnomad ASJ exome

AF:

0.460

Gnomad EAS exome

AF:

0.554

Gnomad SAS exome

AF:

0.656

Gnomad FIN exome

AF:

0.509

Gnomad NFE exome

AF:

0.503

Gnomad OTH exome

AF:

0.524

GnomAD4 exome

AF:

0.513

AC:

721736

AN:

1406678

Hom.:

188104

Cov.:

AF XY:

0.516

AC XY:

359477

AN XY:

696134

show subpopulations

Gnomad4 AFR exome

AF:

0.785

Gnomad4 AMR exome

AF:

0.544

Gnomad4 ASJ exome

AF:

0.464

Gnomad4 EAS exome

AF:

0.524

Gnomad4 SAS exome

AF:

0.640

Gnomad4 FIN exome

AF:

0.492

Gnomad4 NFE exome

AF:

0.495

Gnomad4 OTH exome

AF:

0.532

GnomAD4 genome

AF:

0.580

AC:

88252

AN:

152098

Hom.:

26835

Cov.:

AF XY:

0.581

AC XY:

43204

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.768

Gnomad4 AMR

AF:

0.564

Gnomad4 ASJ

AF:

0.458

Gnomad4 EAS

AF:

0.543

Gnomad4 SAS

AF:

0.652

Gnomad4 FIN

AF:

0.510

Gnomad4 NFE

AF:

0.489

Gnomad4 OTH

AF:

0.553

Alfa

AF:

0.445

Hom.:

2878

Bravo

AF:

0.584

Asia WGS

AF:

0.673

AC:

2343

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

-0.90

CADD

Benign

0.97

DANN

Benign

0.37

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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