1-12941560-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001010889.2(PRAMEF6):c.293G>T(p.Trp98Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 (★).
Frequency
Consequence
NM_001010889.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRAMEF6 | ENST00000376189.5 | c.293G>T | p.Trp98Leu | missense_variant | Exon 3 of 4 | 1 | NM_001010889.2 | ENSP00000365360.1 | ||
PRAMEF6 | ENST00000415464.6 | c.293G>T | p.Trp98Leu | missense_variant | Exon 3 of 4 | 1 | ENSP00000401281.2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 83442Hom.: 0 Cov.: 11 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 8.09e-7 AC: 1AN: 1236736Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 619630
GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 83442Hom.: 0 Cov.: 11 AF XY: 0.00 AC XY: 0AN XY: 39306
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.293G>T (p.W98L) alteration is located in exon 3 (coding exon 2) of the PRAMEF6 gene. This alteration results from a G to T substitution at nucleotide position 293, causing the tryptophan (W) at amino acid position 98 to be replaced by a leucine (L). 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
Publications
No publications associated with this variant yet.