19-8490913-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_032152.5(PRAM1):c.1717G>A(p.Glu573Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000235 in 1,613,696 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRAM1 | NM_032152.5 | c.1717G>A | p.Glu573Lys | missense_variant | Exon 6 of 10 | ENST00000423345.5 | NP_115528.4 | |
PRAM1 | XM_011528352.3 | c.1723G>A | p.Glu575Lys | missense_variant | Exon 6 of 9 | XP_011526654.1 | ||
PRAM1 | XM_005272502.3 | c.1717G>A | p.Glu573Lys | missense_variant | Exon 6 of 9 | XP_005272559.1 | ||
PRAM1 | XM_011528353.3 | c.1723G>A | p.Glu575Lys | missense_variant | Exon 6 of 10 | XP_011526655.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRAM1 | ENST00000423345.5 | c.1717G>A | p.Glu573Lys | missense_variant | Exon 6 of 10 | 1 | NM_032152.5 | ENSP00000408342.2 | ||
PRAM1 | ENST00000594696.1 | n.1007G>A | non_coding_transcript_exon_variant | Exon 2 of 6 | 5 | |||||
PRAM1 | ENST00000599698.5 | n.-38G>A | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249040Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135128
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461400Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 726996
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1717G>A (p.E573K) alteration is located in exon 6 (coding exon 6) of the PRAM1 gene. This alteration results from a G to A substitution at nucleotide position 1717, causing the glutamic acid (E) at amino acid position 573 to be replaced by a lysine (K). 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