8-39920101-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002164.6(IDO1):c.424C>A(p.Pro142Thr) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,610,202 control chromosomes in the GnomAD database, with no homozygous occurrence. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P142L) has been classified as Benign.
Frequency
Consequence
NM_002164.6 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDO1 | NM_002164.6 | c.424C>A | p.Pro142Thr | missense_variant, splice_region_variant | 5/10 | ENST00000518237.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDO1 | ENST00000518237.6 | c.424C>A | p.Pro142Thr | missense_variant, splice_region_variant | 5/10 | 1 | NM_002164.6 | P1 | |
ENST00000517623.1 | n.256-16080G>T | intron_variant, non_coding_transcript_variant | 4 | ||||||
ENST00000522970.1 | n.256+534G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247794Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134406
GnomAD4 exome AF: 0.0000206 AC: 30AN: 1458068Hom.: 0 Cov.: 28 AF XY: 0.0000179 AC XY: 13AN XY: 725358
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 07, 2022 | The c.424C>A (p.P142T) alteration is located in exon 5 (coding exon 5) of the IDO1 gene. This alteration results from a C to A substitution at nucleotide position 424, causing the proline (P) at amino acid position 142 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at