rs8177374
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001318777.2(TIRAP):c.539C>T(p.Ser180Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,613,956 control chromosomes in the GnomAD database, including 18,397 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001318777.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TIRAP | NM_001318777.2 | c.539C>T | p.Ser180Leu | missense_variant | Exon 4 of 5 | ENST00000392679.6 | NP_001305706.1 | |
TIRAP | NM_001318776.2 | c.539C>T | p.Ser180Leu | missense_variant | Exon 4 of 4 | NP_001305705.1 | ||
TIRAP | NM_148910.3 | c.539C>T | p.Ser180Leu | missense_variant | Exon 5 of 5 | NP_683708.1 | ||
TIRAP | NM_001039661.2 | c.539C>T | p.Ser180Leu | missense_variant | Exon 5 of 6 | NP_001034750.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.111 AC: 16910AN: 152142Hom.: 1228 Cov.: 32
GnomAD3 exomes AF: 0.124 AC: 30945AN: 250244Hom.: 2234 AF XY: 0.130 AC XY: 17565AN XY: 135440
GnomAD4 exome AF: 0.148 AC: 216650AN: 1461696Hom.: 17169 Cov.: 34 AF XY: 0.149 AC XY: 108156AN XY: 727136
GnomAD4 genome AF: 0.111 AC: 16904AN: 152260Hom.: 1228 Cov.: 32 AF XY: 0.111 AC XY: 8291AN XY: 74450
ClinVar
Submissions by phenotype
not provided Benign:2
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This variant is associated with the following publications: (PMID: 26771213, 20525286, 22683004, 18417424, 19456234, 18305471, 22058078, 19509334, 21705416, 17322885, 25003251, 26885859, 27166096, 24067789, 23047423, 26614847, 20797905) -
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 24% of patients studied by a panel of primary immunodeficiencies. Number of patients: 21. Only high quality variants are reported. -
Bacteremia, susceptibility Benign:1
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Invasive pneumococcal disease, protection against Benign:1
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Mycobacterium tuberculosis, protection against Benign:1
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Malaria, resistance to Benign:1
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Mycobacterium tuberculosis, susceptibility to;C1970028:Malaria, susceptibility to;C3280645:Bacteremia, susceptibility to, 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at