20-2836296-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022760.6(PCED1A):āc.860G>Cā(p.Trp287Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,614,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_022760.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCED1A | NM_022760.6 | c.860G>C | p.Trp287Ser | missense_variant | 7/8 | ENST00000360652.7 | NP_073597.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCED1A | ENST00000360652.7 | c.860G>C | p.Trp287Ser | missense_variant | 7/8 | 1 | NM_022760.6 | ENSP00000353868 | P1 | |
PCED1A | ENST00000356872.7 | c.707G>C | p.Trp236Ser | missense_variant | 7/8 | 2 | ENSP00000349334 | |||
PCED1A | ENST00000474714.5 | c.136-587G>C | intron_variant | 3 | ENSP00000474824 | |||||
PCED1A | ENST00000487501.2 | n.245-186G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 248980Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134794
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461828Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 727206
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.860G>C (p.W287S) alteration is located in exon 7 (coding exon 6) of the PCED1A gene. This alteration results from a G to C substitution at nucleotide position 860, causing the tryptophan (W) at amino acid position 287 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