NM_032152.5:c.1439G>A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032152.5(PRAM1):c.1439G>A(p.Arg480Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,459,752 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032152.5 missense
Scores
Clinical Significance
Conservation
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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.1439G>A | p.Arg480Gln | missense_variant | Exon 3 of 10 | ENST00000423345.5 | NP_115528.4 | |
PRAM1 | XM_011528352.3 | c.1445G>A | p.Arg482Gln | missense_variant | Exon 3 of 9 | XP_011526654.1 | ||
PRAM1 | XM_005272502.3 | c.1439G>A | p.Arg480Gln | missense_variant | Exon 3 of 9 | XP_005272559.1 | ||
PRAM1 | XM_011528353.3 | c.1445G>A | p.Arg482Gln | missense_variant | Exon 3 of 10 | XP_011526655.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243596Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132674
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1459752Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 726020
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1439G>A (p.R480Q) alteration is located in exon 3 (coding exon 3) of the PRAM1 gene. This alteration results from a G to A substitution at nucleotide position 1439, causing the arginine (R) at amino acid position 480 to be replaced by a glutamine (Q). 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