11-126292802-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_001318777.2(TIRAP):c.393C>T(p.Ser131Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000778 in 1,612,934 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001318777.2 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TIRAP | NM_001318777.2 | c.393C>T | p.Ser131Ser | synonymous_variant | Exon 4 of 5 | ENST00000392679.6 | NP_001305706.1 | |
TIRAP | NM_001318776.2 | c.393C>T | p.Ser131Ser | synonymous_variant | Exon 4 of 4 | NP_001305705.1 | ||
TIRAP | NM_148910.3 | c.393C>T | p.Ser131Ser | synonymous_variant | Exon 5 of 5 | NP_683708.1 | ||
TIRAP | NM_001039661.2 | c.393C>T | p.Ser131Ser | synonymous_variant | Exon 5 of 6 | NP_001034750.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00422 AC: 643AN: 152206Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00110 AC: 273AN: 248160Hom.: 2 AF XY: 0.000855 AC XY: 115AN XY: 134470
GnomAD4 exome AF: 0.000417 AC: 609AN: 1460610Hom.: 3 Cov.: 34 AF XY: 0.000366 AC XY: 266AN XY: 726564
GnomAD4 genome AF: 0.00424 AC: 646AN: 152324Hom.: 6 Cov.: 32 AF XY: 0.00430 AC XY: 320AN XY: 74492
ClinVar
Submissions by phenotype
TIRAP-related disorder Benign:1
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