rs3924112

Positions:

• chr4-38794189-C-T

Variant summary

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

The XR_925163.3(TLR1):​n.3175G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,154 control chromosomes in the GnomAD database, including 2,152 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 0.14 (2152 hom., cov: 32)
• Consequence: TLR1 XR_925163.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637

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=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLR1	XR_925163.3	n.3175G>A		non_coding_transcript_exon_variant	5/5
TLR1	XR_007057953.1	n.2658+2182G>A		intron_variant, non_coding_transcript_variant
TLR1	XR_007057954.1	n.2566+2182G>A		intron_variant, non_coding_transcript_variant
TLR1	XR_925165.3	n.2735+2182G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TLR1	ENST00000505744.5	n.236-2958G>A		intron_variant, non_coding_transcript_variant		3
TLR1	ENST00000510552.1	n.97+348G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21938 AN: 152036 Hom.: 2152 Cov.: 32

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.0797

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.144 AC: 21930 AN: 152154 Hom.: 2152 Cov.: 32 AF XY: 0.143 AC XY: 10614 AN XY: 74378

Gnomad4 AFR AF: 0.0340

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.0797

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.198

Alfa AF: 0.150 Hom.: 271

Bravo AF: 0.150

Asia WGS AF: 0.227 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	15
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3924112; hg19: chr4-38795810;