chr3-179875420-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_016559.3(PEX5L):c.563C>A(p.Thr188Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00121 in 1,610,988 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016559.3 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 |
---|---|---|---|---|---|---|---|
PEX5L | NM_016559.3 | c.563C>A | p.Thr188Asn | missense_variant | 6/15 | ENST00000467460.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX5L | ENST00000467460.6 | c.563C>A | p.Thr188Asn | missense_variant | 6/15 | 1 | NM_016559.3 | A1 | |
PEX5L-AS1 | ENST00000466064.1 | n.45G>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000988 AC: 150AN: 151876Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000764 AC: 192AN: 251460Hom.: 1 AF XY: 0.000728 AC XY: 99AN XY: 135910
GnomAD4 exome AF: 0.00123 AC: 1792AN: 1458992Hom.: 4 Cov.: 32 AF XY: 0.00122 AC XY: 883AN XY: 725844
GnomAD4 genome ? AF: 0.000987 AC: 150AN: 151996Hom.: 1 Cov.: 31 AF XY: 0.000942 AC XY: 70AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | The c.563C>A (p.T188N) alteration is located in exon 6 (coding exon 6) of the PEX5L gene. This alteration results from a C to A substitution at nucleotide position 563, causing the threonine (T) at amino acid position 188 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