Variant chr1-2559503-C-A 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.305-320C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 1,472,328 control chromosomes in the GnomAD database, including 191,666 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 0.54 ( 22913 hom., cov: 34)

Exomes 𝑓: 0.50 ( 168753 hom. )

Consequence

TNFRSF14
NM_003820.4 intron

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: -1.90

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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 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.305-320C>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.305-320C>A		intron_variant		1	NM_003820.4	ENSP00000347948	P1	Q92956-1

Frequencies

GnomAD3 genomes

AF:

0.543

AC:

82469

AN:

151920

Hom.:

22890

Cov.:

show subpopulations

Gnomad AFR

AF:

0.655

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.550

Gnomad ASJ

AF:

0.456

Gnomad EAS

AF:

0.503

Gnomad SAS

AF:

0.641

Gnomad FIN

AF:

0.508

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.483

Gnomad OTH

AF:

0.521

GnomAD3 exomes

AF:

0.525

AC:

70597

AN:

134594

Hom.:

18852

AF XY:

0.528

AC XY:

38669

AN XY:

73300

show subpopulations

Gnomad AFR exome

AF:

0.659

Gnomad AMR exome

AF:

0.532

Gnomad ASJ exome

AF:

0.454

Gnomad EAS exome

AF:

0.498

Gnomad SAS exome

AF:

0.636

Gnomad FIN exome

AF:

0.484

Gnomad NFE exome

AF:

0.479

Gnomad OTH exome

AF:

0.505

GnomAD4 exome

AF:

0.503

AC:

663495

AN:

1320290

Hom.:

168753

Cov.:

AF XY:

0.506

AC XY:

328096

AN XY:

648554

show subpopulations

Gnomad4 AFR exome

AF:

0.661

Gnomad4 AMR exome

AF:

0.531

Gnomad4 ASJ exome

AF:

0.462

Gnomad4 EAS exome

AF:

0.493

Gnomad4 SAS exome

AF:

0.626

Gnomad4 FIN exome

AF:

0.481

Gnomad4 NFE exome

AF:

0.489

Gnomad4 OTH exome

AF:

0.516

GnomAD4 genome

AF:

0.543

AC:

82536

AN:

152038

Hom.:

22913

Cov.:

AF XY:

0.545

AC XY:

40536

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.655

Gnomad4 AMR

AF:

0.550

Gnomad4 ASJ

AF:

0.456

Gnomad4 EAS

AF:

0.503

Gnomad4 SAS

AF:

0.642

Gnomad4 FIN

AF:

0.508

Gnomad4 NFE

AF:

0.483

Gnomad4 OTH

AF:

0.525

Alfa

AF:

0.438

Hom.:

3679

Bravo

AF:

0.542

Asia WGS

AF:

0.637

AC:

2216

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

-0.92

CADD

Benign

0.62

DANN

Benign

0.26

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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