chr11-126290892-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001318777.2(TIRAP):c.-3G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000157 in 1,603,510 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001318777.2 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TIRAP | NM_001318777.2 | c.-3G>A | 5_prime_UTR_variant | Exon 3 of 5 | ENST00000392679.6 | NP_001305706.1 | ||
TIRAP | NM_001318776.2 | c.-3G>A | 5_prime_UTR_variant | Exon 3 of 4 | NP_001305705.1 | |||
TIRAP | NM_148910.3 | c.-3G>A | 5_prime_UTR_variant | Exon 4 of 5 | NP_683708.1 | |||
TIRAP | NM_001039661.2 | c.-3G>A | 5_prime_UTR_variant | Exon 4 of 6 | NP_001034750.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000612 AC: 93AN: 152068Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000191 AC: 45AN: 235070Hom.: 0 AF XY: 0.000118 AC XY: 15AN XY: 126728
GnomAD4 exome AF: 0.000110 AC: 159AN: 1451324Hom.: 0 Cov.: 31 AF XY: 0.0000985 AC XY: 71AN XY: 720834
GnomAD4 genome AF: 0.000611 AC: 93AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.000645 AC XY: 48AN XY: 74392
ClinVar
Submissions by phenotype
TIRAP-related disorder Benign:1
This variant is classified as likely 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