1-12793292-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_023013.4(PRAMEF1):c.65C>T(p.Ala22Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000746 in 1,607,940 control chromosomes in the GnomAD database, including 40 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A22T) has been classified as Uncertain significance.
Frequency
Consequence
NM_023013.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000537 AC: 81AN: 150856Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000432 AC: 107AN: 247494Hom.: 1 AF XY: 0.000463 AC XY: 62AN XY: 133978
GnomAD4 exome AF: 0.000767 AC: 1118AN: 1456966Hom.: 39 Cov.: 34 AF XY: 0.000741 AC XY: 537AN XY: 724702
GnomAD4 genome AF: 0.000537 AC: 81AN: 150974Hom.: 1 Cov.: 31 AF XY: 0.000380 AC XY: 28AN XY: 73688
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.65C>T (p.A22V) 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 65, causing the alanine (A) at amino acid position 22 to be replaced by a valine (V). 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