rs1100886

chr1-223119290-C-Achr1-223119290-C-Gchr1-223119290-C-T

Variant summary

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

The NM_003268.6(TLR5):c.-4-6255G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 151,958 control chromosomes in the GnomAD database, including 35,549 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 0.67 (35549 hom., cov: 31)
• Consequence: TLR5 NM_003268.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883

Genes affected

TLR5 (HGNC:11851): (toll like receptor 5) This gene encodes a member of the toll-like receptor (TLR) family, which plays a fundamental role in pathogen recognition and activation of innate immune responses. These receptors recognize distinct pathogen-associated molecular patterns that are expressed on infectious agents. The protein encoded by this gene recognizes bacterial flagellin, the principal component of bacterial flagella and a virulence factor. The activation of this receptor mobilizes the nuclear factor NF-kappaB, which in turn activates a host of inflammatory-related target genes. Mutations in this gene have been associated with both resistance and susceptibility to systemic lupus erythematosus, and susceptibility to Legionnaire disease.[provided by RefSeq, Dec 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLR5	NM_003268.6	c.-4-6255G>T		intron_variant		ENST00000642603.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TLR5	ENST00000642603.2	c.-4-6255G>T		intron_variant			NM_003268.6	P1
TLR5	ENST00000407096.6	c.-4-6255G>T		intron_variant		3
TLR5	ENST00000540964.5	c.-4-6255G>T		intron_variant		5		P1
TLR5	ENST00000645434.1	c.-4-6255G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101620 AN: 151840 Hom.: 35512 Cov.: 31

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.669 AC: 101712 AN: 151958 Hom.: 35549 Cov.: 31 AF XY: 0.666 AC XY: 49434 AN XY: 74254

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.662

Alfa AF: 0.591 Hom.: 12012

Bravo AF: 0.696

Asia WGS AF: 0.699 AC: 2430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.1
Dann	Benign	0.52

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: rs1100886; hg19: chr1-223292632; COSMIC: COSV60558288; COSMIC: COSV60558288;