chr1-12793480-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_023013.4(PRAMEF1):c.253C>T(p.Leu85Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000087 in 1,608,718 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_023013.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151060Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 247430Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134396
GnomAD4 exome AF: 0.00000823 AC: 12AN: 1457658Hom.: 0 Cov.: 34 AF XY: 0.00000552 AC XY: 4AN XY: 725068
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151060Hom.: 0 Cov.: 31 AF XY: 0.0000136 AC XY: 1AN XY: 73670
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.253C>T (p.L85F) alteration is located in exon 2 (coding exon 1) of the PRAMEF1 gene. This alteration results from a C to T substitution at nucleotide position 253, causing the leucine (L) at amino acid position 85 to be replaced by a phenylalanine (F). 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