6-32822322-G-GAAA
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_018833.3(TAP2):c.1933-5_1933-4insTTT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,326,688 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.0000070 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000030 ( 0 hom. )
Consequence
TAP2
NM_018833.3 splice_region, splice_polypyrimidine_tract, intron
NM_018833.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.143
Genes affected
TAP2 (HGNC:44): (transporter 2, ATP binding cassette subfamily B member) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MDR/TAP subfamily. Members of the MDR/TAP subfamily are involved in multidrug resistance. This gene is located 7 kb telomeric to gene family member ABCB2. The protein encoded by this gene is involved in antigen presentation. This protein forms a heterodimer with ABCB2 in order to transport peptides from the cytoplasm to the endoplasmic reticulum. Mutations in this gene may be associated with ankylosing spondylitis, insulin-dependent diabetes mellitus, and celiac disease. Alternative splicing of this gene produces products which differ in peptide selectivity and level of restoration of surface expression of MHC class I molecules. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 6-32822322-G-GAAA is Benign according to our data. Variant chr6-32822322-G-GAAA is described in ClinVar as [Likely_benign]. Clinvar id is 3042978.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TAP2 | NM_018833.3 | c.1933-5_1933-4insTTT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NP_061313.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TAP2 | ENST00000652259.1 | c.1933-5_1933-4insTTT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENSP00000498827 |
Frequencies
GnomAD3 genomes AF: 0.00000695 AC: 1AN: 143850Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.0000304 AC: 36AN: 1182838Hom.: 0 Cov.: 27 AF XY: 0.0000256 AC XY: 15AN XY: 585392
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GnomAD4 genome AF: 0.00000695 AC: 1AN: 143850Hom.: 0 Cov.: 31 AF XY: 0.0000143 AC XY: 1AN XY: 69708
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
TAP2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 25, 2019 | 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
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at