rs5741881
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_016562.4(TLR7):āc.3087A>Gā(p.Leu1029=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0114 in 1,209,543 control chromosomes in the GnomAD database, including 968 homozygotes. There are 3,635 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.059 ( 461 hom., 1735 hem., cov: 23)
Exomes š: 0.0066 ( 507 hom. 1900 hem. )
Consequence
TLR7
NM_016562.4 synonymous
NM_016562.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.04
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
Variant X-12888595-A-G is Benign according to our data. Variant chrX-12888595-A-G is described in ClinVar as [Benign]. Clinvar id is 2039041.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.04 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR7 | NM_016562.4 | c.3087A>G | p.Leu1029= | synonymous_variant | 3/3 | ENST00000380659.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR7 | ENST00000380659.4 | c.3087A>G | p.Leu1029= | synonymous_variant | 3/3 | 1 | NM_016562.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0590 AC: 6581AN: 111530Hom.: 461 Cov.: 23 AF XY: 0.0509 AC XY: 1718AN XY: 33734
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GnomAD3 exomes AF: 0.0173 AC: 3166AN: 183196Hom.: 212 AF XY: 0.0118 AC XY: 799AN XY: 67646
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GnomAD4 exome AF: 0.00656 AC: 7198AN: 1097959Hom.: 507 Cov.: 32 AF XY: 0.00523 AC XY: 1900AN XY: 363319
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GnomAD4 genome ? AF: 0.0591 AC: 6600AN: 111584Hom.: 461 Cov.: 23 AF XY: 0.0513 AC XY: 1735AN XY: 33798
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at