X-12919685-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_138636.5(TLR8):c.645C>T(p.His215=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 1,097,286 control chromosomes in the GnomAD database, including 74,596 homozygotes. There are 160,196 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.54 ( 12589 hom., 17416 hem., cov: 22)
Exomes 𝑓: 0.44 ( 74596 hom. 160196 hem. )
Failed GnomAD Quality Control
Consequence
TLR8
NM_138636.5 synonymous
NM_138636.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.52
Genes affected
TLR8 (HGNC:15632): (toll like receptor 8) 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 predominantly expressed in lung and peripheral blood leukocytes, and lies in close proximity to another family member, TLR7, on chromosome X. [provided by RefSeq, Jul 2008]
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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=-0.79).
BP6
?
Variant X-12919685-C-T is Benign according to our data. Variant chrX-12919685-C-T is described in ClinVar as [Benign]. Clinvar id is 2688009.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-4.52 with no splicing effect.
BA1
?
GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR8 | NM_138636.5 | c.645C>T | p.His215= | synonymous_variant | 2/2 | ENST00000218032.7 | |
TLR8-AS1 | NR_030727.1 | n.241-11352G>A | intron_variant, non_coding_transcript_variant | ||||
TLR8 | NM_016610.4 | c.699C>T | p.His233= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR8 | ENST00000218032.7 | c.645C>T | p.His215= | synonymous_variant | 2/2 | 1 | NM_138636.5 | P2 | |
TLR8 | ENST00000311912.5 | c.699C>T | p.His233= | synonymous_variant | 3/3 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.539 AC: 59381AN: 110085Hom.: 12582 Cov.: 22 AF XY: 0.537 AC XY: 17356AN XY: 32329
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GnomAD3 exomes AF: 0.524 AC: 95416AN: 182112Hom.: 17853 AF XY: 0.510 AC XY: 34158AN XY: 66926
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GnomAD4 exome AF: 0.438 AC: 480707AN: 1097286Hom.: 74596 Cov.: 34 AF XY: 0.442 AC XY: 160196AN XY: 362736
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.540 AC: 59447AN: 110139Hom.: 12589 Cov.: 22 AF XY: 0.538 AC XY: 17416AN XY: 32393
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 73% of patients studied by a panel of primary immunodeficiencies. Number of patients: 69. Only high quality variants are reported. - |
Computational scores
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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