4-38803084-G-A

Position:

• chr4-38803084-G-A

Variant summary

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

The NM_003263.4(TLR1):​c.-160+1222C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0712 in 152,218 control chromosomes in the GnomAD database, including 993 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 0.071 (993 hom., cov: 32)
• Consequence: TLR1 NM_003263.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLR1	NM_003263.4	c.-160+1222C>T		intron_variant		ENST00000308979.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TLR1	ENST00000308979.7	c.-160+1222C>T		intron_variant		1	NM_003263.4	P1

Frequencies

GnomAD3 genomes AF: 0.0711 AC: 10818 AN: 152100 Hom.: 989 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0772

Gnomad FIN AF: 0.00509

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00178

Gnomad OTH AF: 0.0616

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

GnomAD4 genome AF: 0.0712 AC: 10841 AN: 152218 Hom.: 993 Cov.: 32 AF XY: 0.0756 AC XY: 5625 AN XY: 74424

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0766

Gnomad4 FIN AF: 0.00509

Gnomad4 NFE AF: 0.00178

Gnomad4 OTH AF: 0.0638

Alfa AF: 0.00708 Hom.: 8

Bravo AF: 0.0882

Asia WGS AF: 0.113 AC: 391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.65

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: rs5743578; hg19: chr4-38804705;