rs770150271
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_003190.5(TAPBP):c.1300+3_1300+6delAAGT variant causes a splice region, intron change. The variant allele was found at a frequency of 0.0000415 in 1,612,838 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003190.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TAPBP | NM_003190.5 | c.1300+3_1300+6delAAGT | splice_region_variant, intron_variant | Intron 6 of 7 | ENST00000434618.7 | NP_003181.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000396 AC: 6AN: 151466Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000599 AC: 15AN: 250542Hom.: 0 AF XY: 0.0000738 AC XY: 10AN XY: 135420
GnomAD4 exome AF: 0.0000411 AC: 60AN: 1461254Hom.: 0 AF XY: 0.0000426 AC XY: 31AN XY: 726906
GnomAD4 genome AF: 0.0000462 AC: 7AN: 151584Hom.: 0 Cov.: 31 AF XY: 0.0000810 AC XY: 6AN XY: 74086
ClinVar
Submissions by phenotype
MHC class I deficiency Uncertain:1
This sequence change falls in intron 6 of the TAPBP gene. It does not directly change the encoded amino acid sequence of the TAPBP protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs770150271, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with TAPBP-related conditions. ClinVar contains an entry for this variant (Variation ID: 649689). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at