rs140196414
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_000383.4(AIRE):c.599C>T(p.Pro200Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,612,758 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P200P) has been classified as Likely benign.
Frequency
Consequence
NM_000383.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIRE | NM_000383.4 | c.599C>T | p.Pro200Leu | missense_variant | 5/14 | ENST00000291582.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIRE | ENST00000291582.6 | c.599C>T | p.Pro200Leu | missense_variant | 5/14 | 1 | NM_000383.4 | P1 | |
AIRE | ENST00000527919.5 | n.1143C>T | non_coding_transcript_exon_variant | 4/14 | 2 | ||||
AIRE | ENST00000530812.5 | n.1151C>T | non_coding_transcript_exon_variant | 4/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000355 AC: 54AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000160 AC: 40AN: 250276Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135614
GnomAD4 exome AF: 0.0000767 AC: 112AN: 1460422Hom.: 0 Cov.: 31 AF XY: 0.0000661 AC XY: 48AN XY: 726528
GnomAD4 genome ? AF: 0.000354 AC: 54AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74490
ClinVar
Submissions by phenotype
Polyglandular autoimmune syndrome, type 1 Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Mar 05, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at