chr4-38825899-C-T

Variant names:

• chr4-38825899-C-T
• rs5743828
• NM_006068.5:c.*1184G>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.*1184G>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 0.202 in 152,452 control chromosomes in the GnomAD database, including 3,994 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 0.20 (3988 hom., cov: 32)
  • Exomes 𝑓: 0.14 (6 hom.)
• Consequence: TLR6 NM_006068.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.28 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.*1184G>A		3_prime_UTR	Exon 2 of 2	NP_006059.2
	TLR6	NM_001394553.1		c.*1184G>A		3_prime_UTR	Exon 2 of 2	NP_001381482.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLR6	ENST00000508254.6	TSL:1 MANE Select	c.*1184G>A		3_prime_UTR	Exon 2 of 2	ENSP00000424718.2
	TLR1	ENST00000506146.5	TSL:4	c.-352-20706G>A		intron	N/A	ENSP00000423725.1

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30758 AN: 151940 Hom.: 3984 Cov.: 32

Gnomad AFR AF: 0.0997

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0221

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.169

GnomAD4 exome AF: 0.137 AC: 54 AN: 394 Hom.: 6 Cov.: 0 AF XY: 0.158 AC XY: 32 AN XY: 202

African (AFR) AF: 0.00 AC: 0 AN: 8

American (AMR) AF: 0.00 AC: 0 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.0500 AC: 1 AN: 20

East Asian (EAS) AF: 0.0385 AC: 2 AN: 52

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.304 AC: 14 AN: 46

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.142 AC: 33 AN: 232

Other (OTH) AF: 0.167 AC: 4 AN: 24

GnomAD4 genome AF: 0.202 AC: 30777 AN: 152058 Hom.: 3988 Cov.: 32 AF XY: 0.199 AC XY: 14799 AN XY: 74306

African (AFR) AF: 0.100 AC: 4160 AN: 41540

American (AMR) AF: 0.108 AC: 1651 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3466

East Asian (EAS) AF: 0.0224 AC: 116 AN: 5186

South Asian (SAS) AF: 0.129 AC: 620 AN: 4820

European-Finnish (FIN) AF: 0.360 AC: 3790 AN: 10524

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.284 AC: 19270 AN: 67910

Other (OTH) AF: 0.168 AC: 354 AN: 2112

Alfa AF: 0.243 Hom.: 822

Bravo AF: 0.180

Asia WGS AF: 0.0770 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.46
DANN	Benign	0.71
PhyloP100		-1.2
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: rs5743828; hg19: chr4-38827520;