rs5743558

Positions:

• chr4-38804814-A-AAG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000505940.1(TLR1):​c.-129_-128insCT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,236 control chromosomes in the GnomAD database, including 2,231 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.15 (2231 hom., cov: 30)
  • Failed GnomAD Quality Control
• Consequence: TLR1 ENST00000505940.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307

Genes affected

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLR1	NM_003263.4			upstream_gene_variant		ENST00000308979.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TLR1	ENST00000308979.7			upstream_gene_variant		1	NM_003263.4	P1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22230 AN: 152118 Hom.: 2231 Cov.: 30

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0838

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.205

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.146 AC: 22223 AN: 152236 Hom.: 2231 Cov.: 30 AF XY: 0.145 AC XY: 10776 AN XY: 74422

Gnomad4 AFR AF: 0.0343

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.0838

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.202

Alfa AF: 0.148 Hom.: 230

Bravo AF: 0.152

Asia WGS AF: 0.235 AC: 816 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BranchPoint Hunter		5.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5743558; hg19: chr4-38806435;