4-38792853-TTATATATATATA-TTATATA

Variant names:

• chr4-38792853-TTATATA-T
• rs72518392
• XR_925163.3:n.4505_4510delTATATA

Variant summary

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

The XR_925163.3(TLR1):​n.4505_4510delTATATA 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 0.0417 in 122,240 control chromosomes in the GnomAD database, including 475 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.042 (475 hom., cov: 24)
• Consequence: TLR1 XR_925163.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

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 (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TLR1	XR_925163.3	n.4505_4510delTATATA		non_coding_transcript_exon_variant	Exon 5 of 5
TLR1	XR_007057953.1	n.2659-1628_2659-1623delTATATA		intron_variant	Intron 3 of 3
TLR1	XR_007057954.1	n.2567-1628_2567-1623delTATATA		intron_variant	Intron 2 of 2
TLR1	XR_925165.3	n.2736-1628_2736-1623delTATATA		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TLR1	ENST00000505744.5	n.236-1628_236-1623delTATATA		intron_variant	Intron 3 of 3	3
TLR1	ENST00000510552.1	n.98-1628_98-1623delTATATA		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0415 AC: 5068 AN: 122204 Hom.: 466 Cov.: 24

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0161

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000265

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00439

Gnomad NFE AF: 0.000352

Gnomad OTH AF: 0.0309

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

GnomAD4 genome AF: 0.0417 AC: 5095 AN: 122240 Hom.: 475 Cov.: 24 AF XY: 0.0401 AC XY: 2377 AN XY: 59252

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.0161

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000352

Gnomad4 OTH AF: 0.0308

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;