chr16-284721-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006849.4(PDIA2):c.469C>T(p.Arg157Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000162 in 1,570,174 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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
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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.469C>T | p.Arg157Trp | missense_variant | 3/11 | ENST00000219406.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDIA2 | ENST00000219406.11 | c.469C>T | p.Arg157Trp | missense_variant | 3/11 | 1 | NM_006849.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152154Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000301 AC: 59AN: 196214Hom.: 0 AF XY: 0.000241 AC XY: 26AN XY: 107768
GnomAD4 exome AF: 0.000157 AC: 223AN: 1417902Hom.: 1 Cov.: 71 AF XY: 0.000164 AC XY: 115AN XY: 702122
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152272Hom.: 0 Cov.: 34 AF XY: 0.000134 AC XY: 10AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2021 | The c.469C>T (p.R157W) alteration is located in exon 3 (coding exon 3) of the PDIA2 gene. This alteration results from a C to T substitution at nucleotide position 469, causing the arginine (R) at amino acid position 157 to be replaced by a tryptophan (W). 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