chr4-38797918-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003263.4(TLR1):c.914A>T(p.His305Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0276 in 1,614,120 control chromosomes in the GnomAD database, including 836 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). 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. H305Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_003263.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR1 | NM_003263.4 | c.914A>T | p.His305Leu | missense_variant | 4/4 | ENST00000308979.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR1 | ENST00000308979.7 | c.914A>T | p.His305Leu | missense_variant | 4/4 | 1 | NM_003263.4 | P1 | |
TLR1 | ENST00000502213.6 | c.914A>T | p.His305Leu | missense_variant | 3/3 | 1 | P1 | ||
TLR1 | ENST00000505744.5 | n.235+2939A>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0382 AC: 5809AN: 152174Hom.: 161 Cov.: 32
GnomAD3 exomes AF: 0.0273 AC: 6835AN: 250542Hom.: 143 AF XY: 0.0262 AC XY: 3555AN XY: 135576
GnomAD4 exome AF: 0.0265 AC: 38768AN: 1461828Hom.: 675 Cov.: 36 AF XY: 0.0261 AC XY: 18965AN XY: 727204
GnomAD4 genome AF: 0.0382 AC: 5819AN: 152292Hom.: 161 Cov.: 32 AF XY: 0.0367 AC XY: 2736AN XY: 74488
ClinVar
Submissions by phenotype
TLR1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 31, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at