rs1100886

Variant names:

• chr1-223119290-C-A
• rs1100886
• NM_003268.6:c.-4-6255G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-223119290-C-A
• chr1-223119290-C-G
• chr1-223119290-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TLR5	NM_003268.6	c.-4-6255G>T		intron_variant	Intron 5 of 5	ENST00000642603.2	NP_003259.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TLR5	ENST00000642603.2	c.-4-6255G>T		intron_variant	Intron 5 of 5		NM_003268.6	ENSP00000496355.1

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

African (AFR) AF: 0.877 AC: 36371 AN: 41470

American (AMR) AF: 0.678 AC: 10344 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2083 AN: 3470

East Asian (EAS) AF: 0.790 AC: 4077 AN: 5158

South Asian (SAS) AF: 0.571 AC: 2741 AN: 4802

European-Finnish (FIN) AF: 0.507 AC: 5341 AN: 10528

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.570 AC: 38720 AN: 67956

Other (OTH) AF: 0.662 AC: 1400 AN: 2114

Alfa AF: 0.582 Hom.: 16020

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
PhyloP100		-0.88
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: rs1100886; hg19: chr1-223292632; COSMIC: COSV60558288; COSMIC: COSV60558288;