rs530978
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015225.3(PRUNE2):c.3011C>T(p.Thr1004Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 1,612,692 control chromosomes in the GnomAD database, including 264,258 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_015225.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRUNE2 | NM_015225.3 | c.3011C>T | p.Thr1004Met | missense_variant | 8/19 | ENST00000376718.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRUNE2 | ENST00000376718.8 | c.3011C>T | p.Thr1004Met | missense_variant | 8/19 | 5 | NM_015225.3 | P1 | |
PCA3 | ENST00000644657.1 | n.736+3707G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.493 AC: 74880AN: 151856Hom.: 20352 Cov.: 31
GnomAD3 exomes AF: 0.562 AC: 139824AN: 248656Hom.: 41131 AF XY: 0.567 AC XY: 76553AN XY: 135112
GnomAD4 exome AF: 0.573 AC: 837139AN: 1460718Hom.: 243908 Cov.: 56 AF XY: 0.574 AC XY: 417060AN XY: 726722
GnomAD4 genome ? AF: 0.493 AC: 74893AN: 151974Hom.: 20350 Cov.: 31 AF XY: 0.493 AC XY: 36571AN XY: 74240
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at