21-44288406-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_000383.4(AIRE):c.600G>A(p.Pro200=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000509 in 1,612,506 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 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIRE | NM_000383.4 | c.600G>A | p.Pro200= | synonymous_variant | 5/14 | ENST00000291582.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIRE | ENST00000291582.6 | c.600G>A | p.Pro200= | synonymous_variant | 5/14 | 1 | NM_000383.4 | P1 | |
AIRE | ENST00000527919.5 | n.1144G>A | non_coding_transcript_exon_variant | 4/14 | 2 | ||||
AIRE | ENST00000530812.5 | n.1152G>A | non_coding_transcript_exon_variant | 4/12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000639 AC: 16AN: 250212Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135580
GnomAD4 exome AF: 0.0000418 AC: 61AN: 1460300Hom.: 0 Cov.: 31 AF XY: 0.0000413 AC XY: 30AN XY: 726480
GnomAD4 genome AF: 0.000138 AC: 21AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.000215 AC XY: 16AN XY: 74350
ClinVar
Submissions by phenotype
Polyglandular autoimmune syndrome, type 1 Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 28, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at