chr1-203483227-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002725.4(PRELP):c.43G>A(p.Ala15Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000343 in 1,575,804 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_002725.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRELP | NM_002725.4 | c.43G>A | p.Ala15Thr | missense_variant | 2/3 | ENST00000343110.3 | |
PRELP | NM_201348.2 | c.43G>A | p.Ala15Thr | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRELP | ENST00000343110.3 | c.43G>A | p.Ala15Thr | missense_variant | 2/3 | 1 | NM_002725.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151948Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000546 AC: 12AN: 219764Hom.: 0 AF XY: 0.0000587 AC XY: 7AN XY: 119256
GnomAD4 exome AF: 0.0000358 AC: 51AN: 1423738Hom.: 0 Cov.: 31 AF XY: 0.0000425 AC XY: 30AN XY: 706074
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152066Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 30, 2023 | The c.43G>A (p.A15T) alteration is located in exon 2 (coding exon 1) of the PRELP gene. This alteration results from a G to A substitution at nucleotide position 43, causing the alanine (A) at amino acid position 15 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