16-284757-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006849.4(PDIA2):c.505G>A(p.Gly169Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000761 in 1,563,300 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 Uncertain significance (★).
Frequency
Consequence
NM_006849.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDIA2 | NM_006849.4 | c.505G>A | p.Gly169Ser | missense_variant | 3/11 | ENST00000219406.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDIA2 | ENST00000219406.11 | c.505G>A | p.Gly169Ser | missense_variant | 3/11 | 1 | NM_006849.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000348 AC: 53AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000968 AC: 19AN: 196200Hom.: 0 AF XY: 0.0000653 AC XY: 7AN XY: 107126
GnomAD4 exome AF: 0.0000468 AC: 66AN: 1410996Hom.: 0 Cov.: 56 AF XY: 0.0000444 AC XY: 31AN XY: 697574
GnomAD4 genome ? AF: 0.000348 AC: 53AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.000295 AC XY: 22AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.505G>A (p.G169S) alteration is located in exon 3 (coding exon 3) of the PDIA2 gene. This alteration results from a G to A substitution at nucleotide position 505, causing the glycine (G) at amino acid position 169 to be replaced by a serine (S). 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