chr4-38796673-T-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003263.4(TLR1):c.2159A>C(p.His720Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00674 in 1,614,174 control chromosomes in the GnomAD database, including 56 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 Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003263.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR1 | NM_003263.4 | c.2159A>C | p.His720Pro | missense_variant | 4/4 | ENST00000308979.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR1 | ENST00000308979.7 | c.2159A>C | p.His720Pro | missense_variant | 4/4 | 1 | NM_003263.4 | P1 | |
TLR1 | ENST00000502213.6 | c.2159A>C | p.His720Pro | missense_variant | 3/3 | 1 | P1 | ||
TLR1 | ENST00000505744.5 | n.235+4184A>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00501 AC: 763AN: 152168Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00636 AC: 1600AN: 251446Hom.: 6 AF XY: 0.00648 AC XY: 880AN XY: 135894
GnomAD4 exome AF: 0.00692 AC: 10120AN: 1461888Hom.: 51 Cov.: 30 AF XY: 0.00699 AC XY: 5083AN XY: 727244
GnomAD4 genome ? AF: 0.00502 AC: 764AN: 152286Hom.: 5 Cov.: 32 AF XY: 0.00442 AC XY: 329AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | TLR1: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at