X-12886851-C-T

Position:

chrX-12886851-C-T

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_016562.4(TLR7):c.1343C>T(p.Ala448Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00416 in 1,208,256 control chromosomes in the GnomAD database, including 24 homozygotes. There are 1,602 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0028 ( 1 hom., 71 hem., cov: 23)

Exomes 𝑓: 0.0043 ( 23 hom. 1531 hem. )

Consequence

TLR7
NM_016562.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.592

Variant links:

Genes affected

TLR7 (HGNC:15631): (toll like receptor 7) The protein encoded by this gene is a member of the Toll-like receptor (TLR) family which plays a fundamental role in pathogen recognition and activation of innate immunity. TLRs are highly conserved from Drosophila to humans and share structural and functional similarities. The human TLR family comprises 11 members. They recognize pathogen-associated molecular patterns (PAMPs) that are expressed on infectious agents, and mediate the production of cytokines necessary for the development of effective immunity. For the recognition of structural components in foreign microorganisms, the various TLRs exhibit different patterns of expression as well; in this way for example, TLR-3, -7, and -8 are essential in the recognition of single-stranded RNA viruses. TLR7 senses single-stranded RNA oligonucleotides containing guanosine- and uridine-rich sequences from RNA viruses, a recognition occuring in the endosomes of plasmacytoid dendritic cells and B cells. This gene is predominantly expressed in lung, placenta, and spleen, and is phylogenetically related and lies in close proximity to another family member, TLR8, on chromosome X. [provided by RefSeq, Aug 2020]

TLR7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0049847364).

BP6

Variant X-12886851-C-T is Benign according to our data. Variant chrX-12886851-C-T is described in ClinVar as [Benign]. Clinvar id is 787154.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-12886851-C-T is described in Lovd as [Likely_benign].

BS2

High Hemizygotes in GnomAd4 at 71 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TLR7	NM_016562.4 linkuse as main transcript	c.1343C>T	p.Ala448Val	missense_variant	3/3	ENST00000380659.4	NP_057646.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TLR7	ENST00000380659.4 linkuse as main transcript	c.1343C>T	p.Ala448Val	missense_variant	3/3	1	NM_016562.4	ENSP00000370034	P1

Frequencies

GnomAD3 genomes

AF:

0.00284

AC:

317

AN:

111780

Hom.:

Cov.:

AF XY:

0.00209

AC XY:

AN XY:

33992

show subpopulations

Gnomad AFR

AF:

0.000618

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00295

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00167

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00468

Gnomad OTH

AF:

0.00532

GnomAD3 exomes

AF:

0.00290

AC:

525

AN:

181053

Hom.:

AF XY:

0.00270

AC XY:

180

AN XY:

66687

show subpopulations

Gnomad AFR exome

AF:

0.000479

Gnomad AMR exome

AF:

0.00327

Gnomad ASJ exome

AF:

0.000539

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00157

Gnomad NFE exome

AF:

0.00465

Gnomad OTH exome

AF:

0.00539

GnomAD4 exome

AF:

0.00429

AC:

4708

AN:

1096425

Hom.:

Cov.:

AF XY:

0.00423

AC XY:

1531

AN XY:

361869

show subpopulations

Gnomad4 AFR exome

AF:

0.000569

Gnomad4 AMR exome

AF:

0.00322

Gnomad4 ASJ exome

AF:

0.000671

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000186

Gnomad4 FIN exome

AF:

0.00195

Gnomad4 NFE exome

AF:

0.00514

Gnomad4 OTH exome

AF:

0.00350

GnomAD4 genome

AF:

0.00283

AC:

317

AN:

111831

Hom.:

Cov.:

AF XY:

0.00208

AC XY:

AN XY:

34053

show subpopulations

Gnomad4 AFR

AF:

0.000617

Gnomad4 AMR

AF:

0.00295

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00167

Gnomad4 NFE

AF:

0.00468

Gnomad4 OTH

AF:

0.00526

Alfa

AF:

0.00414

Hom.:

Bravo

AF:

0.00268

TwinsUK

AF:

0.00566

AC:

ALSPAC

AF:

0.00346

AC:

ESP6500AA

AF:

0.000783

AC:

ESP6500EA

AF:

0.00402

AC:

ExAC

AF:

0.00314

AC:

381

EpiCase

AF:

0.00545

EpiControl

AF:

0.00462

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2024	TLR7: BP4, BS1, BS2 -

TLR7-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 04, 2024

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.080

BayesDel_addAF

Benign

-0.79

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.8

DANN

Benign

0.91

DEOGEN2

Benign

0.11

FATHMM_MKL

Benign

0.36

LIST_S2

Benign

0.56

M_CAP

Uncertain

0.10

MetaRNN

Benign

0.0050

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.73

MutationTaster

Benign

1.0

PrimateAI

Benign

0.21

PROVEAN

Benign

-0.74

REVEL

Benign

0.029

Sift

Benign

0.32

Sift4G

Benign

0.29

Polyphen

0.023

Vest4

0.021

MVP

0.38

MPC

0.70

ClinPred

0.0018

GERP RS

3.1

Varity_R

0.067

gMVP

0.41

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over