1-223142735-G-C

Position:

• chr1-223142735-G-C

Variant summary

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

The NM_003268.6(TLR5):​c.-555+461C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,850 control chromosomes in the GnomAD database, including 25,396 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 0.57 (25396 hom., cov: 31)
• Consequence: TLR5 NM_003268.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940

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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TLR5	NM_003268.6	c.-555+461C>G		intron_variant		ENST00000642603.2	NP_003259.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TLR5	ENST00000642603.2	c.-555+461C>G		intron_variant			NM_003268.6	ENSP00000496355	P1

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86588 AN: 151732 Hom.: 25388 Cov.: 31

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.571 AC: 86637 AN: 151850 Hom.: 25396 Cov.: 31 AF XY: 0.570 AC XY: 42314 AN XY: 74192

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.573

Alfa AF: 0.528 Hom.: 2684

Bravo AF: 0.590

Asia WGS AF: 0.673 AC: 2342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	12
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5744105; hg19: chr1-223316077; COSMIC: COSV64827105; COSMIC: COSV64827105;