chr16-15031584-T-G
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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.1400-151T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 603,230 control chromosomes in the GnomAD database, including 33,225 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 0.30 ( 7456 hom., cov: 31)
Exomes 𝑓: 0.33 ( 25769 hom. )
Consequence
PDXDC1
NM_015027.4 intron
NM_015027.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0400
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=-0.96).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDXDC1 | NM_015027.4 | c.1400-151T>G | intron_variant | ENST00000396410.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDXDC1 | ENST00000396410.9 | c.1400-151T>G | intron_variant | 1 | NM_015027.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.302 AC: 45825AN: 151858Hom.: 7434 Cov.: 31
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GnomAD4 exome AF: 0.329 AC: 148668AN: 451254Hom.: 25769 AF XY: 0.332 AC XY: 78238AN XY: 235860
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GnomAD4 genome AF: 0.302 AC: 45893AN: 151976Hom.: 7456 Cov.: 31 AF XY: 0.308 AC XY: 22895AN XY: 74268
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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