22-37658876-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020315.5(PDXP):āc.94A>Gā(p.Asn32Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000271 in 1,219,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_020315.5 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 |
---|---|---|---|---|---|---|---|
PDXP | NM_020315.5 | c.94A>G | p.Asn32Asp | missense_variant | 1/2 | ENST00000215904.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDXP | ENST00000215904.7 | c.94A>G | p.Asn32Asp | missense_variant | 1/2 | 1 | NM_020315.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000101 AC: 15AN: 148432Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000695 AC: 2AN: 28778Hom.: 0 AF XY: 0.0000620 AC XY: 1AN XY: 16134
GnomAD4 exome AF: 0.000295 AC: 316AN: 1071522Hom.: 0 Cov.: 31 AF XY: 0.000282 AC XY: 144AN XY: 509864
GnomAD4 genome AF: 0.000101 AC: 15AN: 148432Hom.: 0 Cov.: 32 AF XY: 0.0000691 AC XY: 5AN XY: 72310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 19, 2022 | The c.94A>G (p.N32D) alteration is located in exon 1 (coding exon 1) of the PDXP gene. This alteration results from a A to G substitution at nucleotide position 94, causing the asparagine (N) at amino acid position 32 to be replaced by an aspartic acid (D). 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