20-2835559-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_022760.6(PCED1A):c.1268G>A(p.Gly423Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00037 in 1,614,028 control chromosomes in the GnomAD database, including 2 homozygotes. 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 (★).
Frequency
Consequence
NM_022760.6 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 |
---|---|---|---|---|---|---|---|
PCED1A | NM_022760.6 | c.1268G>A | p.Gly423Glu | missense_variant | 8/8 | ENST00000360652.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCED1A | ENST00000360652.7 | c.1268G>A | p.Gly423Glu | missense_variant | 8/8 | 1 | NM_022760.6 | P1 | |
PCED1A | ENST00000356872.7 | c.1115G>A | p.Gly372Glu | missense_variant | 8/8 | 2 | |||
PCED1A | ENST00000474714.5 | c.287G>A | p.Gly96Glu | missense_variant | 2/2 | 3 | |||
PCED1A | ENST00000487501.2 | n.467G>A | non_coding_transcript_exon_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000136 AC: 34AN: 250906Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135632
GnomAD4 exome AF: 0.000387 AC: 566AN: 1461854Hom.: 2 Cov.: 30 AF XY: 0.000374 AC XY: 272AN XY: 727238
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2023 | The c.1268G>A (p.G423E) alteration is located in exon 8 (coding exon 7) of the PCED1A gene. This alteration results from a G to A substitution at nucleotide position 1268, causing the glycine (G) at amino acid position 423 to be replaced by a glutamic acid (E). 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