20-48636657-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_020820.4(PREX1):c.3973G>A(p.Ala1325Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,609,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PREX1 | NM_020820.4 | c.3973G>A | p.Ala1325Thr | missense_variant | 32/40 | ENST00000371941.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PREX1 | ENST00000371941.4 | c.3973G>A | p.Ala1325Thr | missense_variant | 32/40 | 1 | NM_020820.4 | P1 | |
PREX1 | ENST00000482556.5 | c.1939G>A | p.Ala647Thr | missense_variant, NMD_transcript_variant | 15/22 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000345 AC: 8AN: 231806Hom.: 0 AF XY: 0.0000471 AC XY: 6AN XY: 127436
GnomAD4 exome AF: 0.0000213 AC: 31AN: 1456826Hom.: 0 Cov.: 34 AF XY: 0.0000248 AC XY: 18AN XY: 724548
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.3973G>A (p.A1325T) alteration is located in exon 32 (coding exon 32) of the PREX1 gene. This alteration results from a G to A substitution at nucleotide position 3973, causing the alanine (A) at amino acid position 1325 to be replaced by a threonine (T). 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