4-38792853-TTATATATATATA-TTATATATATATATATATATA

Variant names:

• chr4-38792853-T-TTATATATA
• rs72518392
• XR_925163.3:n.4503_4510dupTATATATA

Variant summary

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

The XR_925163.3(TLR1):​n.4503_4510dupTATATATA 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 0.00199 in 122,246 control chromosomes in the GnomAD database, including 8 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0020 (8 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 243 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TLR1	XR_925163.3	n.4503_4510dupTATATATA		non_coding_transcript_exon_variant	Exon 5 of 5
TLR1	XR_007057953.1	n.2659-1630_2659-1623dupTATATATA		intron_variant	Intron 3 of 3
TLR1	XR_007057954.1	n.2567-1630_2567-1623dupTATATATA		intron_variant	Intron 2 of 2
TLR1	XR_925165.3	n.2736-1630_2736-1623dupTATATATA		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_236-1622insTATATATA		intron_variant	Intron 3 of 3	3
TLR1	ENST00000510552.1	n.98-1623_98-1622insTATATATA		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.00198 AC: 242 AN: 122210 Hom.: 8 Cov.: 24

Gnomad AFR AF: 0.00460

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00260

Gnomad ASJ AF: 0.00152

Gnomad EAS AF: 0.000575

Gnomad SAS AF: 0.00106

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00439

Gnomad NFE AF: 0.000774

Gnomad OTH AF: 0.00253

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

GnomAD4 genome AF: 0.00199 AC: 243 AN: 122246 Hom.: 8 Cov.: 24 AF XY: 0.00182 AC XY: 108 AN XY: 59256

Gnomad4 AFR AF: 0.00465

Gnomad4 AMR AF: 0.00259

Gnomad4 ASJ AF: 0.00152

Gnomad4 EAS AF: 0.000577

Gnomad4 SAS AF: 0.00106

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000774

Gnomad4 OTH AF: 0.00251

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;