NM_016562.4:c.4-5615C>T

Variant names:

• chrX-12879897-C-T
• rs1620233
• NM_016562.4:c.4-5615C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016562.4(TLR7):​c.4-5615C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 110,585 control chromosomes in the GnomAD database, including 2,979 homozygotes. There are 6,323 hemizygotes in GnomAD. 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 0.21 (2979 hom., 6323 hem., cov: 22)
• Consequence: TLR7 NM_016562.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 8 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):

• systemic lupus erythematosus 17

  Inheritance: XL Classification: MODERATE Submitted by: PanelApp Australia, Baylor College of Medicine Research Center, ClinGen
• immunodeficiency 74, COVID-19-related, X-linked

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

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

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.4-5615C>T		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.4-5615C>T		intron	N/A	ENSP00000370034.3	Q9NYK1

Frequencies

GnomAD3 genomes AF: 0.205 AC: 22687 AN: 110533 Hom.: 2980 Cov.: 22

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.0739

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0524

Gnomad SAS AF: 0.0572

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.176

Gnomad NFE AF: 0.0927

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.205 AC: 22720 AN: 110585 Hom.: 2979 Cov.: 22 AF XY: 0.192 AC XY: 6323 AN XY: 32883

African (AFR) AF: 0.486 AC: 14660 AN: 30187

American (AMR) AF: 0.112 AC: 1159 AN: 10394

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 537 AN: 2636

East Asian (EAS) AF: 0.0531 AC: 189 AN: 3556

South Asian (SAS) AF: 0.0577 AC: 153 AN: 2651

European-Finnish (FIN) AF: 0.126 AC: 737 AN: 5852

Middle Eastern (MID) AF: 0.179 AC: 39 AN: 218

European-Non Finnish (NFE) AF: 0.0927 AC: 4905 AN: 52907

Other (OTH) AF: 0.193 AC: 291 AN: 1507

Alfa AF: 0.123 Hom.: 2909

Bravo AF: 0.220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.69
DANN	Benign	0.36
PhyloP100		-0.078
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

Other links and lift over

dbSNP: rs1620233; hg19: chrX-12898016;