NM_032152.5:c.1390G>T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032152.5(PRAM1):c.1390G>T(p.Val464Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000211 in 1,424,948 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V464M) has been classified as Uncertain significance.
Frequency
Consequence
NM_032152.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRAM1 | NM_032152.5 | c.1390G>T | p.Val464Leu | missense_variant | Exon 2 of 10 | ENST00000423345.5 | NP_115528.4 | |
PRAM1 | XM_011528352.3 | c.1396G>T | p.Val466Leu | missense_variant | Exon 2 of 9 | XP_011526654.1 | ||
PRAM1 | XM_005272502.3 | c.1390G>T | p.Val464Leu | missense_variant | Exon 2 of 9 | XP_005272559.1 | ||
PRAM1 | XM_011528353.3 | c.1396G>T | p.Val466Leu | missense_variant | Exon 2 of 10 | XP_011526655.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000211 AC: 3AN: 1424948Hom.: 0 Cov.: 32 AF XY: 0.00000284 AC XY: 2AN XY: 704686
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.