rs10759933

Positions:

• chr9-117708094-A-C

Variant summary

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

The NM_138554.5(TLR4):​c.94-469A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0664 in 718,130 control chromosomes in the GnomAD database, including 1,919 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 0.081 (610 hom., cov: 32)
  • Exomes 𝑓: 0.063 (1309 hom.)
• Consequence: TLR4 NM_138554.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539

Genes affected

TLR4 (HGNC:11850): (toll like receptor 4) 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 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. In silico studies have found a particularly strong binding of surface TLR4 with the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus disease-2019 (COVID-19). This receptor has also been implicated in signal transduction events induced by lipopolysaccharide (LPS) found in most gram-negative bacteria. Mutations in this gene have been associated with differences in LPS responsiveness, and with susceptibility to age-related macular degeneration. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2020]

RNU6-1082P (HGNC:48045): (RNA, U6 small nuclear 1082, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLR4	NM_138554.5	c.94-469A>C		intron_variant		ENST00000355622.8
TLR4	NM_003266.4	c.-147-105A>C		intron_variant
TLR4	NM_138557.3	c.-341+3529A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TLR4	ENST00000355622.8	c.94-469A>C		intron_variant		1	NM_138554.5	P1
TLR4	ENST00000394487.5	c.-147-105A>C		intron_variant		1
TLR4	ENST00000472304.2	c.93+3529A>C		intron_variant		1
RNU6-1082P	ENST00000364574.1	n.9T>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0806 AC: 12257 AN: 152138 Hom.: 612 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0533

Gnomad ASJ AF: 0.0530

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0951

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0621

Gnomad OTH AF: 0.0719

GnomAD4 exome AF: 0.0626 AC: 35447 AN: 565874 Hom.: 1309 Cov.: 8 AF XY: 0.0624 AC XY: 16604 AN XY: 266284

Gnomad4 AFR exome AF: 0.143

Gnomad4 AMR exome AF: 0.0371

Gnomad4 ASJ exome AF: 0.0541

Gnomad4 EAS exome AF: 0.00105

Gnomad4 SAS exome AF: 0.100

Gnomad4 FIN exome AF: 0.0944

Gnomad4 NFE exome AF: 0.0603

Gnomad4 OTH exome AF: 0.0744

GnomAD4 genome AF: 0.0806 AC: 12270 AN: 152256 Hom.: 610 Cov.: 32 AF XY: 0.0830 AC XY: 6178 AN XY: 74448

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.0533

Gnomad4 ASJ AF: 0.0530

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0951

Gnomad4 NFE AF: 0.0621

Gnomad4 OTH AF: 0.0712

Alfa AF: 0.0797 Hom.: 73

Bravo AF: 0.0761

Asia WGS AF: 0.0710 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.64

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: rs10759933; hg19: chr9-120470372;