chr22-18936116-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_016335.6(PRODH):c.172G>A(p.Ala58Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_016335.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRODH | NM_016335.6 | c.172G>A | p.Ala58Thr | missense_variant | Exon 1 of 14 | ENST00000357068.11 | NP_057419.5 | |
PRODH | NM_001195226.2 | c.-52+274G>A | intron_variant | Intron 1 of 13 | NP_001182155.2 | |||
PRODH | NM_001368250.2 | c.-52+54G>A | intron_variant | Intron 1 of 13 | NP_001355179.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRODH | ENST00000357068.11 | c.172G>A | p.Ala58Thr | missense_variant | Exon 1 of 14 | 1 | NM_016335.6 | ENSP00000349577.6 | ||
ENSG00000283809 | ENST00000638240.1 | c.514-3557C>T | intron_variant | Intron 4 of 5 | 5 | ENSP00000492446.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 0Hom.: 0 Cov.: 0 FAILED QC
GnomAD3 exomes AF: 0.0188 AC: 1324AN: 70306Hom.: 21 AF XY: 0.0174 AC XY: 713AN XY: 40932
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSRAC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 0Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 0
ClinVar
Submissions by phenotype
not provided Benign:2
This variant is associated with the following publications: (PMID: 20524212, 24842239) -
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Proline dehydrogenase deficiency Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at