chr16-284691-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006849.4(PDIA2):c.439C>G(p.Leu147Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000246 in 1,585,814 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.439C>G | p.Leu147Val | missense_variant | 3/11 | ENST00000219406.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDIA2 | ENST00000219406.11 | c.439C>G | p.Leu147Val | missense_variant | 3/11 | 1 | NM_006849.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152178Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000469 AC: 1AN: 213086Hom.: 0 AF XY: 0.00000853 AC XY: 1AN XY: 117300
GnomAD4 exome AF: 0.0000251 AC: 36AN: 1433636Hom.: 0 Cov.: 70 AF XY: 0.0000239 AC XY: 17AN XY: 711606
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152178Hom.: 0 Cov.: 34 AF XY: 0.0000404 AC XY: 3AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.439C>G (p.L147V) alteration is located in exon 3 (coding exon 3) of the PDIA2 gene. This alteration results from a C to G substitution at nucleotide position 439, causing the leucine (L) at amino acid position 147 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