20-48625893-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_020820.4(PREX1):c.4972G>A(p.Asp1658Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000403 in 1,561,732 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PREX1 | ENST00000371941.4 | c.4972G>A | p.Asp1658Asn | missense_variant | Exon 40 of 40 | 1 | NM_020820.4 | ENSP00000361009.3 | ||
PREX1 | ENST00000482556.5 | n.*390G>A | non_coding_transcript_exon_variant | Exon 22 of 22 | 2 | ENSP00000434632.1 | ||||
PREX1 | ENST00000482556.5 | n.*390G>A | 3_prime_UTR_variant | Exon 22 of 22 | 2 | ENSP00000434632.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000561 AC: 1AN: 178118Hom.: 0 AF XY: 0.0000102 AC XY: 1AN XY: 98294
GnomAD4 exome AF: 0.0000433 AC: 61AN: 1409512Hom.: 0 Cov.: 31 AF XY: 0.0000400 AC XY: 28AN XY: 699670
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4972G>A (p.D1658N) alteration is located in exon 40 (coding exon 40) of the PREX1 gene. This alteration results from a G to A substitution at nucleotide position 4972, causing the aspartic acid (D) at amino acid position 1658 to be replaced by an asparagine (N). 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