rs34132052
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_003190.5(TAPBP):c.1239C>T(p.Ser413Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00647 in 1,613,574 control chromosomes in the GnomAD database, including 632 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_003190.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TAPBP | NM_003190.5 | c.1239C>T | p.Ser413Ser | synonymous_variant | Exon 6 of 8 | ENST00000434618.7 | NP_003181.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0322 AC: 4878AN: 151674Hom.: 293 Cov.: 31
GnomAD3 exomes AF: 0.00869 AC: 2181AN: 251040Hom.: 111 AF XY: 0.00661 AC XY: 897AN XY: 135708
GnomAD4 exome AF: 0.00380 AC: 5557AN: 1461782Hom.: 338 Cov.: 32 AF XY: 0.00336 AC XY: 2442AN XY: 727192
GnomAD4 genome AF: 0.0322 AC: 4890AN: 151792Hom.: 294 Cov.: 31 AF XY: 0.0314 AC XY: 2332AN XY: 74172
ClinVar
Submissions by phenotype
MHC class I deficiency Benign:1
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TAPBP-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