chr16-284557-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006849.4(PDIA2):c.370C>T(p.Arg124Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000912 in 1,612,604 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R124H) has been classified as Uncertain significance.
Frequency
Consequence
NM_006849.4 missense
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 |
---|---|---|---|---|---|---|---|
PDIA2 | NM_006849.4 | c.370C>T | p.Arg124Cys | missense_variant | 2/11 | ENST00000219406.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDIA2 | ENST00000219406.11 | c.370C>T | p.Arg124Cys | missense_variant | 2/11 | 1 | NM_006849.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152248Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000171 AC: 42AN: 245716Hom.: 0 AF XY: 0.000127 AC XY: 17AN XY: 133828
GnomAD4 exome AF: 0.0000870 AC: 127AN: 1460356Hom.: 0 Cov.: 31 AF XY: 0.0000798 AC XY: 58AN XY: 726436
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152248Hom.: 0 Cov.: 34 AF XY: 0.000108 AC XY: 8AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.370C>T (p.R124C) alteration is located in exon 2 (coding exon 2) of the PDIA2 gene. This alteration results from a C to T substitution at nucleotide position 370, causing the arginine (R) at amino acid position 124 to be replaced by a cysteine (C). 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