19-8491105-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_032152.5(PRAM1):c.1629G>A(p.Ala543Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000751 in 1,612,254 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 Likely benign (★).
Frequency
Consequence
NM_032152.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRAM1 | NM_032152.5 | c.1629G>A | p.Ala543Ala | synonymous_variant | Exon 5 of 10 | ENST00000423345.5 | NP_115528.4 | |
PRAM1 | XM_011528352.3 | c.1635G>A | p.Ala545Ala | synonymous_variant | Exon 5 of 9 | XP_011526654.1 | ||
PRAM1 | XM_005272502.3 | c.1629G>A | p.Ala543Ala | synonymous_variant | Exon 5 of 9 | XP_005272559.1 | ||
PRAM1 | XM_011528353.3 | c.1635G>A | p.Ala545Ala | synonymous_variant | Exon 5 of 10 | XP_011526655.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRAM1 | ENST00000423345.5 | c.1629G>A | p.Ala543Ala | synonymous_variant | Exon 5 of 10 | 1 | NM_032152.5 | ENSP00000408342.2 | ||
PRAM1 | ENST00000594696.1 | n.919G>A | non_coding_transcript_exon_variant | Exon 1 of 6 | 5 | |||||
PRAM1 | ENST00000599698.5 | n.-230G>A | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000485 AC: 12AN: 247254Hom.: 0 AF XY: 0.0000446 AC XY: 6AN XY: 134384
GnomAD4 exome AF: 0.0000740 AC: 108AN: 1459942Hom.: 0 Cov.: 33 AF XY: 0.0000743 AC XY: 54AN XY: 726354
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74480
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at