rs7192563
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015027.4(PDXDC1):c.1813-157T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.819 in 634,276 control chromosomes in the GnomAD database, including 215,085 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.78 ( 47628 hom., cov: 33)
Exomes 𝑓: 0.83 ( 167457 hom. )
Consequence
PDXDC1
NM_015027.4 intron
NM_015027.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.48
Genes affected
PDXDC1 (HGNC:28995): (pyridoxal dependent decarboxylase domain containing 1) Enables cadherin binding activity. Predicted to be involved in carboxylic acid metabolic process. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDXDC1 | NM_015027.4 | c.1813-157T>C | intron_variant | ENST00000396410.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDXDC1 | ENST00000396410.9 | c.1813-157T>C | intron_variant | 1 | NM_015027.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.783 AC: 119047AN: 152014Hom.: 47571 Cov.: 33
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GnomAD4 exome AF: 0.831 AC: 400498AN: 482144Hom.: 167457 Cov.: 5 AF XY: 0.828 AC XY: 210017AN XY: 253662
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GnomAD4 genome ? AF: 0.783 AC: 119159AN: 152132Hom.: 47628 Cov.: 33 AF XY: 0.786 AC XY: 58437AN XY: 74376
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at