2-73233156-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032319.3(PRADC1):āc.5T>Cā(p.Val2Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000162 in 1,419,270 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_032319.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRADC1 | NM_032319.3 | c.5T>C | p.Val2Ala | missense_variant | 1/5 | ENST00000258083.3 | |
PRADC1 | NR_144358.1 | n.129T>C | non_coding_transcript_exon_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRADC1 | ENST00000258083.3 | c.5T>C | p.Val2Ala | missense_variant | 1/5 | 1 | NM_032319.3 | P1 | |
PRADC1 | ENST00000470391.1 | n.74T>C | non_coding_transcript_exon_variant | 1/2 | 3 | ||||
PRADC1 | ENST00000480093.1 | n.83T>C | non_coding_transcript_exon_variant | 1/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000120 AC: 15AN: 124948Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000618 AC: 8AN: 1294240Hom.: 0 Cov.: 31 AF XY: 0.00000314 AC XY: 2AN XY: 637184
GnomAD4 genome AF: 0.000120 AC: 15AN: 125030Hom.: 0 Cov.: 32 AF XY: 0.0000984 AC XY: 6AN XY: 60982
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2024 | The c.5T>C (p.V2A) alteration is located in exon 1 (coding exon 1) of the PRADC1 gene. This alteration results from a T to C substitution at nucleotide position 5, causing the valine (V) at amino acid position 2 to be replaced by an alanine (A). 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