Variant rs5743818 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_006068.5(TLR6):c.1932T>G(p.Ala644=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 1,614,050 control chromosomes in the GnomAD database, including 52,605 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.19 ( 3821 hom., cov: 32)

Exomes 𝑓: 0.25 ( 48784 hom. )

Consequence

TLR6
NM_006068.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.13

Variant links:

Genes affected

TLR6 (HGNC:16711): (toll like receptor 6) 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. 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. The various TLRs exhibit different patterns of expression. This receptor functionally interacts with toll-like receptor 2 to mediate cellular response to bacterial lipoproteins. A Ser249Pro polymorphism in the extracellular domain of the encoded protein may be associated with an increased of asthma is some populations.[provided by RefSeq, Jan 2011]

TLR6 links:

TLR1 (HGNC:11847): (toll like receptor 1) 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. 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. The various TLRs exhibit different patterns of expression. This gene is ubiquitously expressed, and at higher levels than other TLR genes. Different length transcripts presumably resulting from use of alternative polyadenylation site, and/or from alternative splicing, have been noted for this gene. [provided by RefSeq, Jul 2008]

TLR1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP7

Synonymous conserved (PhyloP=-2.13 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLR6	NM_006068.5 linkuse as main transcript	c.1932T>G	p.Ala644=	synonymous_variant	2/2	ENST00000508254.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TLR6	ENST00000508254.6 linkuse as main transcript	c.1932T>G	p.Ala644=	synonymous_variant	2/2	1	NM_006068.5	P1	Q9Y2C9-1
TLR6	ENST00000381950.2 linkuse as main transcript	c.1932T>G	p.Ala644=	synonymous_variant	3/3			P1	Q9Y2C9-1
TLR1	ENST00000506146.5 linkuse as main transcript	c.-352-22349T>G		intron_variant		4

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

29103

AN:

152058

Hom.:

3821

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0755

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.0970

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.0135

Gnomad SAS

AF:

0.0918

Gnomad FIN

AF:

0.361

Gnomad MID

AF:

0.121

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.160

GnomAD3 exomes

AF:

0.192

AC:

48312

AN:

251464

Hom.:

6221

AF XY:

0.193

AC XY:

26288

AN XY:

135910

show subpopulations

Gnomad AFR exome

AF:

0.0715

Gnomad AMR exome

AF:

0.0768

Gnomad ASJ exome

AF:

0.184

Gnomad EAS exome

AF:

0.0122

Gnomad SAS exome

AF:

0.105

Gnomad FIN exome

AF:

0.357

Gnomad NFE exome

AF:

0.266

Gnomad OTH exome

AF:

0.201

GnomAD4 exome

AF:

0.245

AC:

358805

AN:

1461874

Hom.:

48784

Cov.:

AF XY:

0.242

AC XY:

176285

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.0718

Gnomad4 AMR exome

AF:

0.0818

Gnomad4 ASJ exome

AF:

0.186

Gnomad4 EAS exome

AF:

0.0115

Gnomad4 SAS exome

AF:

0.106

Gnomad4 FIN exome

AF:

0.350

Gnomad4 NFE exome

AF:

0.275

Gnomad4 OTH exome

AF:

0.220

GnomAD4 genome

AF:

0.191

AC:

29107

AN:

152176

Hom.:

3821

Cov.:

AF XY:

0.188

AC XY:

13979

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.0756

Gnomad4 AMR

AF:

0.0969

Gnomad4 ASJ

AF:

0.171

Gnomad4 EAS

AF:

0.0137

Gnomad4 SAS

AF:

0.0915

Gnomad4 FIN

AF:

0.361

Gnomad4 NFE

AF:

0.280

Gnomad4 OTH

AF:

0.158

Alfa

AF:

0.237

Hom.:

6309

Bravo

AF:

0.168

Asia WGS

AF:

0.0590

AC:

205

AN:

3478

EpiCase

AF:

0.261

EpiControl

AF:

0.243

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.83

DANN

Benign

0.43

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over