6-32829412-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_001290043.2(TAP2):c.1920G>A(p.Gln640=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000671 in 1,604,242 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00051 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00069 ( 1 hom. )
Consequence
TAP2
NM_001290043.2 synonymous
NM_001290043.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0430
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 -9 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
Variant 6-32829412-C-T is Benign according to our data. Variant chr6-32829412-C-T is described in ClinVar as [Benign]. Clinvar id is 534715.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.043 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000505 (77/152344) while in subpopulation AMR AF= 0.00222 (34/15312). AF 95% confidence interval is 0.00163. There are 0 homozygotes in gnomad4. There are 39 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAP2 | NM_001290043.2 | c.1920G>A | p.Gln640= | synonymous_variant | 11/12 | ENST00000374897.4 | |
TAP2 | NM_018833.3 | c.1920G>A | p.Gln640= | synonymous_variant | 11/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAP2 | ENST00000374897.4 | c.1920G>A | p.Gln640= | synonymous_variant | 11/12 | 1 | NM_001290043.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000506 AC: 77AN: 152226Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000623 AC: 146AN: 234268Hom.: 0 AF XY: 0.000666 AC XY: 84AN XY: 126176
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GnomAD4 exome AF: 0.000689 AC: 1000AN: 1451898Hom.: 1 Cov.: 54 AF XY: 0.000692 AC XY: 499AN XY: 721146
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GnomAD4 genome AF: 0.000505 AC: 77AN: 152344Hom.: 0 Cov.: 32 AF XY: 0.000524 AC XY: 39AN XY: 74492
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
MHC class I deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 11, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at