rs2075876
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000383.4(AIRE):c.653-387G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 240,530 control chromosomes in the GnomAD database, including 4,716 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.19 ( 3578 hom., cov: 33)
Exomes 𝑓: 0.13 ( 1138 hom. )
Consequence
AIRE
NM_000383.4 intron
NM_000383.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.00900
Genes affected
AIRE (HGNC:360): (autoimmune regulator) This gene encodes a transcriptional regulator that forms nuclear bodies and interacts with the transcriptional coactivator CREB binding protein. The encoded protein plays an important role in immunity by regulating the expression of autoantigens and negative selection of autoreactive T-cells in the thymus. Mutations in this gene cause the rare autosomal-recessive systemic autoimmune disease termed autoimmune polyendocrinopathy with candidiasis and ectodermal dystrophy (APECED). [provided by RefSeq, Jun 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIRE | NM_000383.4 | c.653-387G>A | intron_variant | ENST00000291582.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIRE | ENST00000291582.6 | c.653-387G>A | intron_variant | 1 | NM_000383.4 | P1 | |||
AIRE | ENST00000527919.5 | n.1239G>A | non_coding_transcript_exon_variant | 5/14 | 2 | ||||
AIRE | ENST00000530812.5 | n.2016G>A | non_coding_transcript_exon_variant | 4/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.193 AC: 28596AN: 148126Hom.: 3557 Cov.: 33
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GnomAD4 exome AF: 0.127 AC: 11714AN: 92288Hom.: 1138 Cov.: 0 AF XY: 0.127 AC XY: 6005AN XY: 47234
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GnomAD4 genome ? AF: 0.193 AC: 28662AN: 148242Hom.: 3578 Cov.: 33 AF XY: 0.196 AC XY: 14248AN XY: 72580
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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