4-38792853-TTATATATATATA-TTATATATATATATA

Variant names:

• chr4-38792853-T-TTA
• rs72518392
• XR_925163.3:n.4509_4510dupTA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The XR_925163.3(TLR1):​n.4509_4510dupTA 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 0.0348 in 122,054 control chromosomes in the GnomAD database, including 328 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.035 (328 hom., cov: 24)
• Consequence: TLR1 XR_925163.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TLR1	XR_925163.3	n.4509_4510dupTA		non_coding_transcript_exon_variant	Exon 5 of 5
TLR1	XR_007057953.1	n.2659-1624_2659-1623dupTA		intron_variant	Intron 3 of 3
TLR1	XR_007057954.1	n.2567-1624_2567-1623dupTA		intron_variant	Intron 2 of 2
TLR1	XR_925165.3	n.2736-1624_2736-1623dupTA		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TLR1	ENST00000505744.5	n.236-1623_236-1622insTA		intron_variant	Intron 3 of 3	3
TLR1	ENST00000510552.1	n.98-1623_98-1622insTA		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0348 AC: 4251 AN: 122018 Hom.: 330 Cov.: 24

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.00287

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.0746

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0537

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

GnomAD4 genome AF: 0.0348 AC: 4249 AN: 122054 Hom.: 328 Cov.: 24 AF XY: 0.0359 AC XY: 2124 AN XY: 59160

Gnomad4 AFR AF: 0.0473

Gnomad4 AMR AF: 0.0311

Gnomad4 ASJ AF: 0.0432

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.0965

Gnomad4 FIN AF: 0.0112

Gnomad4 NFE AF: 0.0190

Gnomad4 OTH AF: 0.0553

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72518392; hg19: chr4-38794474;