rs1003854
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000383.4(AIRE):c.879+156T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 983,106 control chromosomes in the GnomAD database, including 33,164 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.23 ( 4227 hom., cov: 34)
Exomes 𝑓: 0.26 ( 28937 hom. )
Consequence
AIRE
NM_000383.4 intron
NM_000383.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.32
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 21-44290224-T-C is Benign according to our data. Variant chr21-44290224-T-C is described in ClinVar as [Benign]. Clinvar id is 1262941.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIRE | NM_000383.4 | c.879+156T>C | intron_variant | ENST00000291582.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIRE | ENST00000291582.6 | c.879+156T>C | intron_variant | 1 | NM_000383.4 | P1 | |||
AIRE | ENST00000527919.5 | n.1612+156T>C | intron_variant, non_coding_transcript_variant | 2 | |||||
AIRE | ENST00000530812.5 | n.2629+156T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.227 AC: 34449AN: 152076Hom.: 4223 Cov.: 34
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GnomAD4 exome AF: 0.263 AC: 218662AN: 830912Hom.: 28937 Cov.: 23 AF XY: 0.264 AC XY: 101219AN XY: 383814
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GnomAD4 genome ? AF: 0.226 AC: 34446AN: 152194Hom.: 4227 Cov.: 34 AF XY: 0.228 AC XY: 17000AN XY: 74406
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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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