chr1-13416419-C-T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001099852.2(PRAMEF20):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 0.0000186 in 1,613,944 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001099852.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152230Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000103 AC: 11AN: 107226 AF XY: 0.0000540 show subpopulations
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461596Hom.: 0 Cov.: 33 AF XY: 0.0000193 AC XY: 14AN XY: 727094 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74494 show subpopulations
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 PRAMEF20 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