4-38828054-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006068.5(TLR6):c.1420G>A(p.Ala474Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00397 in 1,614,190 control chromosomes in the GnomAD database, including 246 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A474V) has been classified as Likely benign.
Frequency
Consequence
NM_006068.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TLR6 | NM_006068.5 | c.1420G>A | p.Ala474Thr | missense_variant | 2/2 | ENST00000508254.6 | NP_006059.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TLR6 | ENST00000508254.6 | c.1420G>A | p.Ala474Thr | missense_variant | 2/2 | 1 | NM_006068.5 | ENSP00000424718 | P1 | |
TLR6 | ENST00000381950.2 | c.1420G>A | p.Ala474Thr | missense_variant | 3/3 | ENSP00000371376 | P1 | |||
TLR1 | ENST00000506146.5 | c.-352-22861G>A | intron_variant | 4 | ENSP00000423725 |
Frequencies
GnomAD3 genomes AF: 0.0213 AC: 3248AN: 152180Hom.: 120 Cov.: 32
GnomAD3 exomes AF: 0.00559 AC: 1406AN: 251442Hom.: 55 AF XY: 0.00413 AC XY: 561AN XY: 135906
GnomAD4 exome AF: 0.00215 AC: 3146AN: 1461892Hom.: 126 Cov.: 36 AF XY: 0.00182 AC XY: 1324AN XY: 727246
GnomAD4 genome AF: 0.0214 AC: 3257AN: 152298Hom.: 120 Cov.: 32 AF XY: 0.0210 AC XY: 1566AN XY: 74472
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at