4-38792853-TTATATATATATA-TTATA

Variant names:

• chr4-38792853-TTATATATA-T
• rs72518392
• XR_925163.3:n.4503_4510delTATATATA

Variant summary

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

The XR_925163.3(TLR1):​n.4503_4510delTATATATA 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 0.00272 in 122,252 control chromosomes in the GnomAD database, including 14 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0027 (14 hom., cov: 24)
• Consequence: TLR1 XR_925163.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

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 333 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TLR1	XR_925163.3	n.4503_4510delTATATATA		non_coding_transcript_exon_variant	Exon 5 of 5
TLR1	XR_007057953.1	n.2659-1630_2659-1623delTATATATA		intron_variant	Intron 3 of 3
TLR1	XR_007057954.1	n.2567-1630_2567-1623delTATATATA		intron_variant	Intron 2 of 2
TLR1	XR_925165.3	n.2736-1630_2736-1623delTATATATA		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TLR1	ENST00000505744.5	n.236-1630_236-1623delTATATATA		intron_variant	Intron 3 of 3	3
TLR1	ENST00000510552.1	n.98-1630_98-1623delTATATATA		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.00272 AC: 333 AN: 122216 Hom.: 14 Cov.: 24

Gnomad AFR AF: 0.00977

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000419

Gnomad ASJ AF: 0.000381

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000265

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00189

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

GnomAD4 genome AF: 0.00272 AC: 333 AN: 122252 Hom.: 14 Cov.: 24 AF XY: 0.00278 AC XY: 165 AN XY: 59262

Gnomad4 AFR AF: 0.00975

Gnomad4 AMR AF: 0.000418

Gnomad4 ASJ AF: 0.000381

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000266

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00188

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;