20-48627919-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_020820.4(PREX1):c.4811G>A(p.Arg1604Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000757 in 1,452,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020820.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PREX1 | ENST00000371941.4 | c.4811G>A | p.Arg1604Gln | missense_variant | Exon 38 of 40 | 1 | NM_020820.4 | ENSP00000361009.3 | ||
PREX1 | ENST00000482556.5 | n.*229G>A | non_coding_transcript_exon_variant | Exon 20 of 22 | 2 | ENSP00000434632.1 | ||||
PREX1 | ENST00000482556.5 | n.*229G>A | 3_prime_UTR_variant | Exon 20 of 22 | 2 | ENSP00000434632.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249412Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135248
GnomAD4 exome AF: 0.00000757 AC: 11AN: 1452928Hom.: 0 Cov.: 34 AF XY: 0.00000830 AC XY: 6AN XY: 722784
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4811G>A (p.R1604Q) alteration is located in exon 38 (coding exon 38) of the PREX1 gene. This alteration results from a G to A substitution at nucleotide position 4811, causing the arginine (R) at amino acid position 1604 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