Variant 12-6385074-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000228918.9(LTBR):c.246A>G(p.Thr82=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 1,614,226 control chromosomes in the GnomAD database, including 98 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0072 ( 6 hom., cov: 32)

Exomes 𝑓: 0.011 ( 92 hom. )

Consequence

LTBR
ENST00000228918.9 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.21

Variant links:

Genes affected

LTBR (HGNC:6718): (lymphotoxin beta receptor) This gene encodes a member of the tumor necrosis factor receptor superfamily. The major ligands of this receptor include lymphotoxin alpha/beta and tumor necrosis factor ligand superfamily member 14. The encoded protein plays a role in signalling during the development of lymphoid and other organs, lipid metabolism, immune response, and programmed cell death. Activity of this receptor has also been linked to carcinogenesis. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Aug 2012]

LTBR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 12-6385074-A-G is Benign according to our data. Variant chr12-6385074-A-G is described in ClinVar as [Benign]. Clinvar id is 773257.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.21 with no splicing effect.

BS2

High AC in GnomAd4 at 1097 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LTBR	NM_002342.3 linkuse as main transcript	c.246A>G	p.Thr82=	synonymous_variant	3/10	ENST00000228918.9	NP_002333.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LTBR	ENST00000228918.9 linkuse as main transcript	c.246A>G	p.Thr82=	synonymous_variant	3/10	1	NM_002342.3	ENSP00000228918	P2	P36941-1

Frequencies

GnomAD3 genomes

AF:

0.00721

AC:

1097

AN:

152220

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00162

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.00445

Gnomad ASJ

AF:

0.00749

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00289

Gnomad FIN

AF:

0.0173

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0106

Gnomad OTH

AF:

0.00669

GnomAD3 exomes

AF:

0.00822

AC:

2067

AN:

251494

Hom.:

AF XY:

0.00800

AC XY:

1087

AN XY:

135922

show subpopulations

Gnomad AFR exome

AF:

0.00117

Gnomad AMR exome

AF:

0.00194

Gnomad ASJ exome

AF:

0.00853

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00389

Gnomad FIN exome

AF:

0.0188

Gnomad NFE exome

AF:

0.0116

Gnomad OTH exome

AF:

0.00814

GnomAD4 exome

AF:

0.0107

AC:

15661

AN:

1461888

Hom.:

Cov.:

AF XY:

0.0105

AC XY:

7632

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.00134

Gnomad4 AMR exome

AF:

0.00237

Gnomad4 ASJ exome

AF:

0.00849

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00432

Gnomad4 FIN exome

AF:

0.0173

Gnomad4 NFE exome

AF:

0.0121

Gnomad4 OTH exome

AF:

0.00949

GnomAD4 genome

AF:

0.00720

AC:

1097

AN:

152338

Hom.:

Cov.:

AF XY:

0.00721

AC XY:

537

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.00161

Gnomad4 AMR

AF:

0.00444

Gnomad4 ASJ

AF:

0.00749

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00290

Gnomad4 FIN

AF:

0.0173

Gnomad4 NFE

AF:

0.0106

Gnomad4 OTH

AF:

0.00662

Alfa

AF:

0.00882

Hom.:

Bravo

AF:

0.00644

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.00960

EpiControl

AF:

0.00883

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.57

DANN

Benign

0.49

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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