4-38792853-TTATATATATATA-TTATATATATATATATATATATATATATATATA

Variant names:

• chr4-38792853-T-TTATATATATATATATATATA
• rs72518392
• XR_925163.3:n.4491_4510dupTATATATATATATATATATA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The XR_925163.3(TLR1):​n.4491_4510dupTATATATATATATATATATA 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 0.00652 in 122,014 control chromosomes in the GnomAD database, including 22 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0065 (22 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 796 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TLR1	XR_925163.3	n.4491_4510dupTATATATATATATATATATA		non_coding_transcript_exon_variant	Exon 5 of 5
TLR1	XR_007057953.1	n.2659-1642_2659-1623dupTATATATATATATATATATA		intron_variant	Intron 3 of 3
TLR1	XR_007057954.1	n.2567-1642_2567-1623dupTATATATATATATATATATA		intron_variant	Intron 2 of 2
TLR1	XR_925165.3	n.2736-1642_2736-1623dupTATATATATATATATATATA		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_236-1622insTATATATATATATATATATA		intron_variant	Intron 3 of 3	3
TLR1	ENST00000510552.1	n.98-1623_98-1622insTATATATATATATATATATA		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.00653 AC: 796 AN: 121976 Hom.: 22 Cov.: 24

Gnomad AFR AF: 0.0128

Gnomad AMI AF: 0.00143

Gnomad AMR AF: 0.00529

Gnomad ASJ AF: 0.00114

Gnomad EAS AF: 0.00288

Gnomad SAS AF: 0.00771

Gnomad FIN AF: 0.00213

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00419

Gnomad OTH AF: 0.00823

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

GnomAD4 genome AF: 0.00652 AC: 796 AN: 122014 Hom.: 22 Cov.: 24 AF XY: 0.00605 AC XY: 358 AN XY: 59154

Gnomad4 AFR AF: 0.0128

Gnomad4 AMR AF: 0.00528

Gnomad4 ASJ AF: 0.00114

Gnomad4 EAS AF: 0.00289

Gnomad4 SAS AF: 0.00747

Gnomad4 FIN AF: 0.00213

Gnomad4 NFE AF: 0.00419

Gnomad4 OTH AF: 0.00819

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;