20-48627880-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4BS2
The NM_020820.4(PREX1):c.4850C>T(p.Thr1617Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000161 in 1,612,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T1617T) has been classified as Benign.
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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PREX1 | NM_020820.4 | c.4850C>T | p.Thr1617Met | missense_variant | 38/40 | ENST00000371941.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PREX1 | ENST00000371941.4 | c.4850C>T | p.Thr1617Met | missense_variant | 38/40 | 1 | NM_020820.4 | P1 | |
PREX1 | ENST00000482556.5 | c.*268C>T | 3_prime_UTR_variant, NMD_transcript_variant | 20/22 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249770Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135338
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1460702Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 726656
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.4850C>T (p.T1617M) alteration is located in exon 38 (coding exon 38) of the PREX1 gene. This alteration results from a C to T substitution at nucleotide position 4850, causing the threonine (T) at amino acid position 1617 to be replaced by a methionine (M). 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