Variant rs3821985 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.1083C>G(p.Thr361=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 1,612,288 control chromosomes in the GnomAD database, including 105,146 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 0.43 ( 15381 hom., cov: 33)

Exomes 𝑓: 0.35 ( 89765 hom. )

Consequence

TLR6
NM_006068.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.80

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=-0.83).

BP7

Synonymous conserved (PhyloP=-1.8 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TLR6	NM_006068.5 linkuse as main transcript	c.1083C>G	p.Thr361=	synonymous_variant	2/2	ENST00000508254.6	NP_006059.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TLR6	ENST00000508254.6 linkuse as main transcript	c.1083C>G	p.Thr361=	synonymous_variant	2/2	1	NM_006068.5	ENSP00000424718	P1	Q9Y2C9-1
TLR6	ENST00000381950.2 linkuse as main transcript	c.1083C>G	p.Thr361=	synonymous_variant	3/3			ENSP00000371376	P1	Q9Y2C9-1
TLR1	ENST00000506146.5 linkuse as main transcript	c.-352-23198C>G		intron_variant		4		ENSP00000423725

Frequencies

GnomAD3 genomes

AF:

0.428

AC:

65011

AN:

151972

Hom.:

15355

Cov.:

show subpopulations

Gnomad AFR

AF:

0.635

Gnomad AMI

AF:

0.215

Gnomad AMR

AF:

0.337

Gnomad ASJ

AF:

0.322

Gnomad EAS

AF:

0.383

Gnomad SAS

AF:

0.370

Gnomad FIN

AF:

0.417

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.341

Gnomad OTH

AF:

0.389

GnomAD3 exomes

AF:

0.370

AC:

92817

AN:

250914

Hom.:

18020

AF XY:

0.364

AC XY:

49406

AN XY:

135628

show subpopulations

Gnomad AFR exome

AF:

0.644

Gnomad AMR exome

AF:

0.320

Gnomad ASJ exome

AF:

0.335

Gnomad EAS exome

AF:

0.381

Gnomad SAS exome

AF:

0.376

Gnomad FIN exome

AF:

0.412

Gnomad NFE exome

AF:

0.338

Gnomad OTH exome

AF:

0.351

GnomAD4 exome

AF:

0.346

AC:

504804

AN:

1460198

Hom.:

89765

Cov.:

AF XY:

0.346

AC XY:

251376

AN XY:

726034

show subpopulations

Gnomad4 AFR exome

AF:

0.642

Gnomad4 AMR exome

AF:

0.321

Gnomad4 ASJ exome

AF:

0.333

Gnomad4 EAS exome

AF:

0.340

Gnomad4 SAS exome

AF:

0.376

Gnomad4 FIN exome

AF:

0.404

Gnomad4 NFE exome

AF:

0.332

Gnomad4 OTH exome

AF:

0.372

GnomAD4 genome

AF:

0.428

AC:

65087

AN:

152090

Hom.:

15381

Cov.:

AF XY:

0.428

AC XY:

31848

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.635

Gnomad4 AMR

AF:

0.336

Gnomad4 ASJ

AF:

0.322

Gnomad4 EAS

AF:

0.383

Gnomad4 SAS

AF:

0.369

Gnomad4 FIN

AF:

0.417

Gnomad4 NFE

AF:

0.341

Gnomad4 OTH

AF:

0.392

Alfa

AF:

0.297

Hom.:

1246

Bravo

AF:

0.427

EpiCase

AF:

0.335

EpiControl

AF:

0.324

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.4

DANN

Benign

0.73

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