19-35803037-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_021232.2(PRODH2):c.1043G>A(p.Arg348His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000669 in 1,569,676 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_021232.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRODH2 | NM_021232.2 | c.1043G>A | p.Arg348His | missense_variant | Exon 8 of 10 | ENST00000653904.2 | NP_067055.2 | |
PRODH2 | NM_001378292.1 | c.887G>A | p.Arg296His | missense_variant | Exon 7 of 9 | NP_001365221.1 | ||
PRODH2 | NM_001378293.1 | c.1043G>A | p.Arg348His | missense_variant | Exon 8 of 9 | NP_001365222.1 | ||
PRODH2 | NM_001378294.1 | c.887G>A | p.Arg296His | missense_variant | Exon 7 of 8 | NP_001365223.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRODH2 | ENST00000653904.2 | c.1043G>A | p.Arg348His | missense_variant | Exon 8 of 10 | NM_021232.2 | ENSP00000499779.1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152146Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000677 AC: 96AN: 1417530Hom.: 0 Cov.: 30 AF XY: 0.0000586 AC XY: 41AN XY: 699988
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74302
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at