chr4-186079213-C-T

Variant names:

• chr4-186079213-C-T
• rs5743313
• NM_003265.3:c.633+182C>T

Variant summary

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

The NM_003265.3(TLR3):​c.633+182C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 151,898 control chromosomes in the GnomAD database, including 3,049 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 0.19 (3049 hom., cov: 32)
• Consequence: TLR3 NM_003265.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 39 publications found

Genes affected

TLR3 (HGNC:11849): (toll like receptor 3) 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 is most abundantly expressed in placenta and pancreas, and is restricted to the dendritic subpopulation of the leukocytes. It recognizes dsRNA associated with viral infection, and induces the activation of NF-kappaB and the production of type I interferons. It thus plays a role in host defense against multiple viruses. [provided by RefSeq, Jul 2021]

TLR3 Gene-Disease associations (from GenCC):

• immunodeficiency 83, susceptibility to viral infections

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

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 (SAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003265.3. 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
	TLR3	NM_003265.3	MANE Select	c.633+182C>T		intron	N/A	NP_003256.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLR3	ENST00000296795.8	TSL:1 MANE Select	c.633+182C>T		intron	N/A	ENSP00000296795.3
	TLR3	ENST00000513189.1	TSL:1	n.633+182C>T		intron	N/A	ENSP00000423386.1
	TLR3	ENST00000698351.1		c.633+182C>T		intron	N/A	ENSP00000513674.1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29560 AN: 151780 Hom.: 3042 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.195 AC: 29588 AN: 151898 Hom.: 3049 Cov.: 32 AF XY: 0.190 AC XY: 14124 AN XY: 74242

African (AFR) AF: 0.195 AC: 8073 AN: 41412

American (AMR) AF: 0.147 AC: 2252 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3464

East Asian (EAS) AF: 0.120 AC: 616 AN: 5154

South Asian (SAS) AF: 0.245 AC: 1177 AN: 4800

European-Finnish (FIN) AF: 0.114 AC: 1202 AN: 10580

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14402 AN: 67904

Other (OTH) AF: 0.212 AC: 447 AN: 2106

Alfa AF: 0.212 Hom.: 718

Bravo AF: 0.197

Asia WGS AF: 0.180 AC: 627 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	4.0
DANN	Benign	0.73
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: rs5743313; hg19: chr4-187000367;