4-38831106-C-T

Variant names:

• chr4-38831106-C-T
• rs5743794
• NM_006068.5:c.-64-1569G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006068.5(TLR6):​c.-64-1569G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 150,976 control chromosomes in the GnomAD database, including 2,300 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 0.15 (2300 hom., cov: 32)
• Consequence: TLR6 NM_006068.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 22 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006068.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLR6	NM_006068.5	MANE Select	c.-64-1569G>A		intron	N/A	NP_006059.2
	TLR6	NM_001394553.1		c.-64-1569G>A		intron	N/A	NP_001381482.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLR6	ENST00000508254.6	TSL:1 MANE Select	c.-64-1569G>A		intron	N/A	ENSP00000424718.2
	TLR6	ENST00000381950.2	TSL:6	c.-64-1569G>A		intron	N/A	ENSP00000371376.1
	TLR1	ENST00000506146.5	TSL:4	c.-353+25655G>A		intron	N/A	ENSP00000423725.1

Frequencies

GnomAD3 genomes AF: 0.152 AC: 22890 AN: 150896 Hom.: 2301 Cov.: 32

Gnomad AFR AF: 0.0392

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.0840

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.218

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.152 AC: 22886 AN: 150976 Hom.: 2300 Cov.: 32 AF XY: 0.150 AC XY: 11057 AN XY: 73716

African (AFR) AF: 0.0391 AC: 1617 AN: 41306

American (AMR) AF: 0.184 AC: 2793 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1158 AN: 3468

East Asian (EAS) AF: 0.346 AC: 1782 AN: 5148

South Asian (SAS) AF: 0.219 AC: 1050 AN: 4802

European-Finnish (FIN) AF: 0.0840 AC: 837 AN: 9966

Middle Eastern (MID) AF: 0.410 AC: 119 AN: 290

European-Non Finnish (NFE) AF: 0.189 AC: 12823 AN: 67780

Other (OTH) AF: 0.216 AC: 453 AN: 2096

Alfa AF: 0.154 Hom.: 321

Bravo AF: 0.156

Asia WGS AF: 0.222 AC: 773 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.70
PhyloP100		0.18
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5743794; hg19: chr4-38832727;