15-43746549-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005313.5(PDIA3):c.10C>T(p.Arg4Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000063 in 1,603,314 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005313.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDIA3 | NM_005313.5 | c.10C>T | p.Arg4Cys | missense_variant | 1/13 | ENST00000300289.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDIA3 | ENST00000300289.10 | c.10C>T | p.Arg4Cys | missense_variant | 1/13 | 1 | NM_005313.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000826 AC: 19AN: 230140Hom.: 0 AF XY: 0.0000707 AC XY: 9AN XY: 127304
GnomAD4 exome AF: 0.0000593 AC: 86AN: 1450976Hom.: 0 Cov.: 31 AF XY: 0.0000513 AC XY: 37AN XY: 721232
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152338Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2022 | The c.10C>T (p.R4C) alteration is located in exon 1 (coding exon 1) of the PDIA3 gene. This alteration results from a C to T substitution at nucleotide position 10, causing the arginine (R) at amino acid position 4 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