20-48636504-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_020820.4(PREX1):c.4126G>A(p.Val1376Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000441 in 1,609,308 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 Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PREX1 | NM_020820.4 | c.4126G>A | p.Val1376Ile | missense_variant | 32/40 | ENST00000371941.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PREX1 | ENST00000371941.4 | c.4126G>A | p.Val1376Ile | missense_variant | 32/40 | 1 | NM_020820.4 | P1 | |
PREX1 | ENST00000482556.5 | c.2092G>A | p.Val698Ile | missense_variant, NMD_transcript_variant | 15/22 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000107 AC: 25AN: 233724Hom.: 0 AF XY: 0.0000774 AC XY: 10AN XY: 129144
GnomAD4 exome AF: 0.0000378 AC: 55AN: 1456944Hom.: 0 Cov.: 30 AF XY: 0.0000359 AC XY: 26AN XY: 724948
GnomAD4 genome AF: 0.000105 AC: 16AN: 152364Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74508
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 06, 2023 | The c.4126G>A (p.V1376I) 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 4126, causing the valine (V) at amino acid position 1376 to be replaced by an isoleucine (I). 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