rs4833095
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003263.4(TLR1):āc.743A>Gā(p.Asn248Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 1,613,238 control chromosomes in the GnomAD database, including 90,036 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
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.743A>G | p.Asn248Ser | missense_variant | 4/4 | ENST00000308979.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR1 | ENST00000308979.7 | c.743A>G | p.Asn248Ser | missense_variant | 4/4 | 1 | NM_003263.4 | P1 | |
TLR1 | ENST00000502213.6 | c.743A>G | p.Asn248Ser | missense_variant | 3/3 | 1 | P1 | ||
TLR1 | ENST00000505744.5 | n.235+2768A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.436 AC: 66260AN: 152006Hom.: 19203 Cov.: 32
GnomAD3 exomes AF: 0.381 AC: 95308AN: 250080Hom.: 22422 AF XY: 0.374 AC XY: 50670AN XY: 135426
GnomAD4 exome AF: 0.273 AC: 399521AN: 1461114Hom.: 70781 Cov.: 36 AF XY: 0.279 AC XY: 202717AN XY: 726712
GnomAD4 genome AF: 0.436 AC: 66372AN: 152124Hom.: 19255 Cov.: 32 AF XY: 0.435 AC XY: 32398AN XY: 74396
ClinVar
Submissions by phenotype
TLR1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 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). - |
Leprosy, susceptibility to, 5 Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Jun 15, 2009 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at