4-38792853-TTATATATATATA-TTATATATATA

Variant names:

• chr4-38792853-TTA-T
• rs72518392
• XR_925163.3:n.4509_4510delTA

Variant summary

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

The XR_925163.3(TLR1):​n.4509_4510delTA 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 0.049 in 122,024 control chromosomes in the GnomAD database, including 378 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.049 (378 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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TLR1	XR_925163.3	n.4509_4510delTA		non_coding_transcript_exon_variant	Exon 5 of 5
TLR1	XR_007057953.1	n.2659-1624_2659-1623delTA		intron_variant	Intron 3 of 3
TLR1	XR_007057954.1	n.2567-1624_2567-1623delTA		intron_variant	Intron 2 of 2
TLR1	XR_925165.3	n.2736-1624_2736-1623delTA		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TLR1	ENST00000505744.5	n.236-1624_236-1623delTA		intron_variant	Intron 3 of 3	3
TLR1	ENST00000510552.1	n.98-1624_98-1623delTA		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0490 AC: 5978 AN: 121990 Hom.: 378 Cov.: 24

Gnomad AFR AF: 0.0956

Gnomad AMI AF: 0.0215

Gnomad AMR AF: 0.0530

Gnomad ASJ AF: 0.0286

Gnomad EAS AF: 0.0190

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0172

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.0238

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.0490 AC: 5981 AN: 122024 Hom.: 378 Cov.: 24 AF XY: 0.0498 AC XY: 2944 AN XY: 59136

Gnomad4 AFR AF: 0.0958

Gnomad4 AMR AF: 0.0530

Gnomad4 ASJ AF: 0.0286

Gnomad4 EAS AF: 0.0191

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0172

Gnomad4 NFE AF: 0.0238

Gnomad4 OTH AF: 0.0699

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;