rs179010

Variant names:

• chrX-12884766-T-C
• rs179010
• NM_016562.4:c.4-746T>C

Your query was ambiguous. Multiple possible variants found:

• chrX-12884766-T-C
• chrX-12884766-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_016562.4(TLR7):​c.4-746T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.73 (21523 hom., 24154 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: TLR7 NM_016562.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 53 publications found

Genes affected

TLR7 (HGNC:15631): (toll like receptor 7) 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. The human TLR family comprises 11 members. 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. For the recognition of structural components in foreign microorganisms, the various TLRs exhibit different patterns of expression as well; in this way for example, TLR-3, -7, and -8 are essential in the recognition of single-stranded RNA viruses. TLR7 senses single-stranded RNA oligonucleotides containing guanosine- and uridine-rich sequences from RNA viruses, a recognition occuring in the endosomes of plasmacytoid dendritic cells and B cells. This gene is predominantly expressed in lung, placenta, and spleen, and is phylogenetically related and lies in close proximity to another family member, TLR8, on chromosome X. [provided by RefSeq, Aug 2020]

TLR7 Gene-Disease associations (from GenCC):

• immunodeficiency 74, COVID-19-related, X-linked

  Inheritance: XL, Unknown Classification: MODERATE, LIMITED Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae)
• systemic lupus erythematosus 17

  Inheritance: XL Classification: MODERATE Submitted by: PanelApp Australia, Baylor College of Medicine Research Center, ClinGen
• systemic lupus erythematosus

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016562.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLR7	NM_016562.4	MANE Select	c.4-746T>C		intron	N/A	NP_057646.1	B2R9N9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLR7	ENST00000380659.4	TSL:1 MANE Select	c.4-746T>C		intron	N/A	ENSP00000370034.3	Q9NYK1

Frequencies

GnomAD3 genomes AF: 0.734 AC: 81520 AN: 111128 Hom.: 21522 Cov.: 23

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.705

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.734

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.734 AC: 81581 AN: 111183 Hom.: 21523 Cov.: 23 AF XY: 0.724 AC XY: 24154 AN XY: 33371

African (AFR) AF: 0.837 AC: 25611 AN: 30601

American (AMR) AF: 0.816 AC: 8575 AN: 10506

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 1646 AN: 2631

East Asian (EAS) AF: 0.667 AC: 2348 AN: 3522

South Asian (SAS) AF: 0.461 AC: 1232 AN: 2671

European-Finnish (FIN) AF: 0.661 AC: 3912 AN: 5919

Middle Eastern (MID) AF: 0.708 AC: 153 AN: 216

European-Non Finnish (NFE) AF: 0.692 AC: 36622 AN: 52927

Other (OTH) AF: 0.732 AC: 1110 AN: 1517

Alfa AF: 0.714 Hom.: 67778

Bravo AF: 0.758

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.46
PhyloP100		-0.49
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs179010;

hg19: chrX-12902885;