6-32829532-T-G
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001290043.2(TAP2):āc.1800A>Cā(p.Val600Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0508 in 1,613,994 control chromosomes in the GnomAD database, including 2,457 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.064 ( 387 hom., cov: 32)
Exomes š: 0.049 ( 2070 hom. )
Consequence
TAP2
NM_001290043.2 synonymous
NM_001290043.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.01
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 Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
Variant 6-32829532-T-G is Benign according to our data. Variant chr6-32829532-T-G is described in ClinVar as [Benign]. Clinvar id is 403514.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-5.01 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0972 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TAP2 | NM_001290043.2 | c.1800A>C | p.Val600Val | synonymous_variant | 11/12 | ENST00000374897.4 | NP_001276972.1 | |
TAP2 | NM_018833.3 | c.1800A>C | p.Val600Val | synonymous_variant | 11/12 | NP_061313.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TAP2 | ENST00000374897.4 | c.1800A>C | p.Val600Val | synonymous_variant | 11/12 | 1 | NM_001290043.2 | ENSP00000364032.3 | ||
ENSG00000250264 | ENST00000452392.2 | c.1800A>C | p.Val600Val | synonymous_variant | 11/15 | 2 | ENSP00000391806.2 |
Frequencies
GnomAD3 genomes AF: 0.0642 AC: 9766AN: 152078Hom.: 387 Cov.: 32
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GnomAD3 exomes AF: 0.0510 AC: 12810AN: 251306Hom.: 440 AF XY: 0.0497 AC XY: 6744AN XY: 135830
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GnomAD4 exome AF: 0.0494 AC: 72185AN: 1461798Hom.: 2070 Cov.: 39 AF XY: 0.0483 AC XY: 35119AN XY: 727206
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GnomAD4 genome AF: 0.0642 AC: 9769AN: 152196Hom.: 387 Cov.: 32 AF XY: 0.0654 AC XY: 4863AN XY: 74404
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
MHC class I deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
TAP2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 08, 2019 | 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
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BayesDel_noAF
Benign
CADD
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at