7-82758699-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_033026.6(PCLO):c.15305A>G(p.Asn5102Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000207 in 1,447,150 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. N5102N) has been classified as Likely benign.
Frequency
Consequence
NM_033026.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCLO | NM_033026.6 | c.15305A>G | p.Asn5102Ser | missense_variant | 25/25 | ENST00000333891.14 | |
PCLO | XM_047420210.1 | c.15488A>G | p.Asn5163Ser | missense_variant | 26/26 | ||
PCLO | XM_047420211.1 | c.15014A>G | p.Asn5005Ser | missense_variant | 26/26 | ||
PCLO | XM_017012006.3 | c.8393A>G | p.Asn2798Ser | missense_variant | 24/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCLO | ENST00000333891.14 | c.15305A>G | p.Asn5102Ser | missense_variant | 25/25 | 2 | NM_033026.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000207 AC: 3AN: 1447150Hom.: 0 Cov.: 27 AF XY: 0.00000278 AC XY: 2AN XY: 720644
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2022 | The c.15305A>G (p.N5102S) alteration is located in exon 25 (coding exon 25) of the PCLO gene. This alteration results from a A to G substitution at nucleotide position 15305, causing the asparagine (N) at amino acid position 5102 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.