chr16-284749-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006849.4(PDIA2):c.497C>T(p.Ala166Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000179 in 1,563,066 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
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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 |
---|---|---|---|---|---|---|---|
PDIA2 | NM_006849.4 | c.497C>T | p.Ala166Val | missense_variant | 3/11 | ENST00000219406.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDIA2 | ENST00000219406.11 | c.497C>T | p.Ala166Val | missense_variant | 3/11 | 1 | NM_006849.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000363 AC: 7AN: 192756Hom.: 0 AF XY: 0.0000474 AC XY: 5AN XY: 105484
GnomAD4 exome AF: 0.0000163 AC: 23AN: 1410788Hom.: 0 Cov.: 61 AF XY: 0.0000172 AC XY: 12AN XY: 697802
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152278Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.497C>T (p.A166V) 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 497, causing the alanine (A) at amino acid position 166 to be replaced by a valine (V). 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