chr21-44294404-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP3BP6_Very_StrongBS1BS2
The NM_000383.4(AIRE):c.1404G>A(p.Thr468=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00179 in 1,569,294 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T468T) has been classified as Likely benign.
Frequency
Consequence
NM_000383.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIRE | NM_000383.4 | c.1404G>A | p.Thr468= | synonymous_variant | 12/14 | ENST00000291582.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIRE | ENST00000291582.6 | c.1404G>A | p.Thr468= | synonymous_variant | 12/14 | 1 | NM_000383.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00566 AC: 857AN: 151280Hom.: 11 Cov.: 31
GnomAD3 exomes AF: 0.00208 AC: 380AN: 182778Hom.: 6 AF XY: 0.00169 AC XY: 171AN XY: 101034
GnomAD4 exome AF: 0.00138 AC: 1957AN: 1417896Hom.: 13 Cov.: 31 AF XY: 0.00133 AC XY: 937AN XY: 703108
GnomAD4 genome AF: 0.00566 AC: 857AN: 151398Hom.: 11 Cov.: 31 AF XY: 0.00547 AC XY: 405AN XY: 74000
ClinVar
Submissions by phenotype
Polyglandular autoimmune syndrome, type 1 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing;curation | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 18, 2011 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 17, 2020 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | AIRE: BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at