4-38792853-TTATATATATATA-TTATATATATATATATATATATATATATATATATATA

Variant names:

• chr4-38792853-T-TTATATATATATATATATATATATA
• rs72518392
• XR_925163.3:n.4510_4511insTATATATATATATATATATATATA

Variant summary

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

The XR_925163.3(TLR1):​n.4510_4511insTATATATATATATATATATATATA 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 0.0119 in 121,562 control chromosomes in the GnomAD database, including 42 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.012 (42 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 1445 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TLR1	XR_925163.3	n.4510_4511insTATATATATATATATATATATATA		non_coding_transcript_exon_variant	Exon 5 of 5
TLR1	XR_007057953.1	n.2659-1623_2659-1622insTATATATATATATATATATATATA		intron_variant	Intron 3 of 3
TLR1	XR_007057954.1	n.2567-1623_2567-1622insTATATATATATATATATATATATA		intron_variant	Intron 2 of 2
TLR1	XR_925165.3	n.2736-1623_2736-1622insTATATATATATATATATATATATA		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_236-1622insTATATATATATATATATATATATA		intron_variant	Intron 3 of 3	3
TLR1	ENST00000510552.1	n.98-1623_98-1622insTATATATATATATATATATATATA		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0119 AC: 1446 AN: 121526 Hom.: 42 Cov.: 24

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.00835

Gnomad ASJ AF: 0.0257

Gnomad EAS AF: 0.00492

Gnomad SAS AF: 0.0117

Gnomad FIN AF: 0.00326

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0135

Gnomad OTH AF: 0.0127

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

GnomAD4 genome AF: 0.0119 AC: 1445 AN: 121562 Hom.: 42 Cov.: 24 AF XY: 0.0116 AC XY: 685 AN XY: 58926

Gnomad4 AFR AF: 0.0119

Gnomad4 AMR AF: 0.00834

Gnomad4 ASJ AF: 0.0257

Gnomad4 EAS AF: 0.00465

Gnomad4 SAS AF: 0.0118

Gnomad4 FIN AF: 0.00326

Gnomad4 NFE AF: 0.0135

Gnomad4 OTH AF: 0.0126

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;