16-14998375-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015027.4(PDXDC1):c.131C>A(p.Ser44Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,290 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015027.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152290Hom.: 0 Cov.: 49
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250464Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135418
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152290Hom.: 0 Cov.: 49 AF XY: 0.0000269 AC XY: 2AN XY: 74404
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.131C>A (p.S44Y) alteration is located in exon 3 (coding exon 3) of the PDXDC1 gene. This alteration results from a C to A substitution at nucleotide position 131, causing the serine (S) at amino acid position 44 to be replaced by a tyrosine (Y). 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