3-52221285-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017442.4(TLR9):āc.3031A>Gā(p.Met1011Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000655 in 1,526,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_017442.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TLR9 | NM_017442.4 | c.3031A>G | p.Met1011Val | missense_variant | 2/2 | ENST00000360658.3 | NP_059138.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TLR9 | ENST00000360658.3 | c.3031A>G | p.Met1011Val | missense_variant | 2/2 | 1 | NM_017442.4 | ENSP00000353874.2 | ||
ENSG00000173366 | ENST00000494383.1 | c.3490A>G | p.Met1164Val | missense_variant | 5/5 | 2 | ENSP00000417517.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000655 AC: 9AN: 1374772Hom.: 0 Cov.: 30 AF XY: 0.00000889 AC XY: 6AN XY: 674614
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2022 | The c.3031A>G (p.M1011V) alteration is located in exon 2 (coding exon 2) of the TLR9 gene. This alteration results from a A to G substitution at nucleotide position 3031, causing the methionine (M) at amino acid position 1011 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at