rs2381290

Positions:

• chr4-38825193-T-A
• chr4-38825193-T-C
• chr4-38825193-T-G

Variant summary

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

The NM_006068.5(TLR6):​c.*1890A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,102 control chromosomes in the GnomAD database, including 11,780 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 0.37 (11780 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: TLR6 NM_006068.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TLR6	NM_006068.5	c.*1890A>T		3_prime_UTR_variant	2/2	ENST00000508254.6	NP_006059.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TLR6	ENST00000508254	c.*1890A>T		3_prime_UTR_variant	2/2	1	NM_006068.5	ENSP00000424718.2
TLR1	ENST00000506146.5	c.-352-20000A>T		intron_variant		4		ENSP00000423725.1

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56732 AN: 151968 Hom.: 11770 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.407

GnomAD4 exome AF: 0.250 AC: 4 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.373 AC: 56775 AN: 152086 Hom.: 11780 Cov.: 32 AF XY: 0.369 AC XY: 27418 AN XY: 74332

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.406

Alfa AF: 0.326 Hom.: 1040

Bravo AF: 0.357

Asia WGS AF: 0.341 AC: 1184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.44

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: rs2381290; hg19: chr4-38826814;