rs5743827

chr4-38825904-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006068.5(TLR6):c.*1179G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,410 control chromosomes in the GnomAD database, including 5,820 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 0.26 (5814 hom., cov: 32)
  • Exomes 𝑓: 0.18 (6 hom.)
• Consequence: TLR6 NM_006068.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

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]

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLR6	NM_006068.5	c.*1179G>A		3_prime_UTR_variant	2/2	ENST00000508254.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TLR6	ENST00000508254.6	c.*1179G>A		3_prime_UTR_variant	2/2	1	NM_006068.5	P1
TLR1	ENST00000506146.5	c.-352-20711G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39942 AN: 151912 Hom.: 5799 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0989

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.237

GnomAD4 exome AF: 0.175 AC: 67 AN: 382 Hom.: 6 Cov.: 0 AF XY: 0.175 AC XY: 35 AN XY: 200

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.0714

Gnomad4 ASJ exome AF: 0.0625

Gnomad4 EAS exome AF: 0.0926

Gnomad4 FIN exome AF: 0.357

Gnomad4 NFE exome AF: 0.185

Gnomad4 OTH exome AF: 0.0455

GnomAD4 genome AF: 0.263 AC: 40000 AN: 152028 Hom.: 5814 Cov.: 32 AF XY: 0.261 AC XY: 19350 AN XY: 74280

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.0993

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.241

Alfa AF: 0.311 Hom.: 1014

Bravo AF: 0.241

Asia WGS AF: 0.196 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.2
Dann	Benign	0.52

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

Other links and lift over

dbSNP: rs5743827; hg19: chr4-38827525;