chr10-119173798-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_006793.5(PRDX3):āc.386T>Cā(p.Val129Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,612,756 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. V129V) has been classified as Likely benign.
Frequency
Consequence
NM_006793.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDX3 | NM_006793.5 | c.386T>C | p.Val129Ala | missense_variant | 4/7 | ENST00000298510.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDX3 | ENST00000298510.4 | c.386T>C | p.Val129Ala | missense_variant | 4/7 | 1 | NM_006793.5 | P1 | |
PRDX3 | ENST00000463322.1 | n.397T>C | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251394Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135870
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460444Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726588
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74486
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2021 | The c.386T>C (p.V129A) alteration is located in exon 4 (coding exon 4) of the PRDX3 gene. This alteration results from a T to C substitution at nucleotide position 386, causing the valine (V) at amino acid position 129 to be replaced by an alanine (A). 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