chrX-12919119-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_138636.5(TLR8):c.79G>A(p.Glu27Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000123 in 1,210,065 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 49 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_138636.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR8 | NM_138636.5 | c.79G>A | p.Glu27Lys | missense_variant | 2/2 | ENST00000218032.7 | |
TLR8-AS1 | NR_030727.1 | n.241-10786C>T | intron_variant, non_coding_transcript_variant | ||||
TLR8 | NM_016610.4 | c.133G>A | p.Glu45Lys | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR8 | ENST00000218032.7 | c.79G>A | p.Glu27Lys | missense_variant | 2/2 | 1 | NM_138636.5 | P2 | |
TLR8 | ENST00000311912.5 | c.133G>A | p.Glu45Lys | missense_variant | 3/3 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000232 AC: 26AN: 111966Hom.: 0 Cov.: 23 AF XY: 0.000264 AC XY: 9AN XY: 34134
GnomAD3 exomes AF: 0.000164 AC: 30AN: 182900Hom.: 0 AF XY: 0.000118 AC XY: 8AN XY: 67522
GnomAD4 exome AF: 0.000112 AC: 123AN: 1098046Hom.: 0 Cov.: 31 AF XY: 0.000110 AC XY: 40AN XY: 363410
GnomAD4 genome ? AF: 0.000232 AC: 26AN: 112019Hom.: 0 Cov.: 23 AF XY: 0.000263 AC XY: 9AN XY: 34197
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.79G>A (p.E27K) alteration is located in exon 2 (coding exon 2) of the TLR8 gene. This alteration results from a G to A substitution at nucleotide position 79, causing the glutamic acid (E) at amino acid position 27 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | TLR8: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at