1-12793953-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_023013.4(PRAMEF1):āc.326A>Cā(p.Asp109Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000559 in 1,608,966 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_023013.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRAMEF1 | NM_023013.4 | c.326A>C | p.Asp109Ala | missense_variant | 3/4 | ENST00000332296.7 | NP_075389.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRAMEF1 | ENST00000332296.7 | c.326A>C | p.Asp109Ala | missense_variant | 3/4 | 1 | NM_023013.4 | ENSP00000332134 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151248Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1457718Hom.: 1 Cov.: 33 AF XY: 0.00000414 AC XY: 3AN XY: 725100
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151248Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73776
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.326A>C (p.D109A) alteration is located in exon 3 (coding exon 2) of the PRAMEF1 gene. This alteration results from a A to C substitution at nucleotide position 326, causing the aspartic acid (D) at amino acid position 109 to be replaced by an alanine (A). 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