chr16-10876635-C-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000572017.1(ENSG00000262151):n.439-11585G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000933 in 152,276 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: 𝑓 0.00093 ( 0 hom., cov: 33)
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.877
Genes affected
CIITA (HGNC:7067): (class II major histocompatibility complex transactivator) This gene encodes a protein with an acidic transcriptional activation domain, 4 LRRs (leucine-rich repeats) and a GTP binding domain. The protein is located in the nucleus and acts as a positive regulator of class II major histocompatibility complex gene transcription, and is referred to as the "master control factor" for the expression of these genes. The protein also binds GTP and uses GTP binding to facilitate its own transport into the nucleus. Once in the nucleus it does not bind DNA but rather uses an intrinsic acetyltransferase (AT) activity to act in a coactivator-like fashion. Mutations in this gene have been associated with bare lymphocyte syndrome type II (also known as hereditary MHC class II deficiency or HLA class II-deficient combined immunodeficiency), increased susceptibility to rheumatoid arthritis, multiple sclerosis, and possibly myocardial infarction. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CIITA | XM_006720880.4 | c.346+10063C>T | intron_variant | XP_006720943.2 | ||||
| CIITA | XM_011522484.4 | c.346+10063C>T | intron_variant | XP_011520786.1 | ||||
| CIITA | XM_011522485.3 | c.346+10063C>T | intron_variant | XP_011520787.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ENST00000572017.1 | n.439-11585G>A | intron_variant, non_coding_transcript_variant | 3 | |||||||
| CIITA | ENST00000636238.1 | c.-21+10316C>T | intron_variant | 5 | ENSP00000490205 | |||||
| CIITA | ENST00000637439.1 | c.283+10063C>T | intron_variant | 5 | ENSP00000489907 |
Frequencies
GnomAD3 genomes 0.000933 AC: 142AN: 152158Hom.: 0 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.000933 AC: 142AN: 152276Hom.: 0 Cov.: 33 AF XY: 0.000859 AC XY: 64AN XY: 74466
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not provided Other:1
| not provided, no classification provided | literature only | Human Evolutionary Genetics, Institut Pasteur | - | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at