20-48634765-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_020820.4(PREX1):c.4178G>A(p.Arg1393Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,614,064 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_020820.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PREX1 | NM_020820.4 | c.4178G>A | p.Arg1393Gln | missense_variant | 33/40 | ENST00000371941.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PREX1 | ENST00000371941.4 | c.4178G>A | p.Arg1393Gln | missense_variant | 33/40 | 1 | NM_020820.4 | P1 | |
PREX1 | ENST00000482556.5 | c.2144G>A | p.Arg715Gln | missense_variant, NMD_transcript_variant | 16/22 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251368Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135860
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461726Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727164
GnomAD4 genome AF: 0.00000656 AC: 1AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.4178G>A (p.R1393Q) alteration is located in exon 33 (coding exon 33) of the PREX1 gene. This alteration results from a G to A substitution at nucleotide position 4178, causing the arginine (R) at amino acid position 1393 to be replaced by a glutamine (Q). 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