chr20-2836048-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022760.6(PCED1A):c.1108C>T(p.Pro370Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000015 in 1,332,358 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCED1A | NM_022760.6 | c.1108C>T | p.Pro370Ser | 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.1108C>T | p.Pro370Ser | missense_variant | 7/8 | 1 | NM_022760.6 | ENSP00000353868 | P1 | |
PCED1A | ENST00000356872.7 | c.955C>T | p.Pro319Ser | missense_variant | 7/8 | 2 | ENSP00000349334 | |||
PCED1A | ENST00000474714.5 | c.136-339C>T | intron_variant | 3 | ENSP00000474824 | |||||
PCED1A | ENST00000487501.2 | n.307C>T | non_coding_transcript_exon_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000150 AC: 2AN: 1332358Hom.: 0 Cov.: 35 AF XY: 0.00000154 AC XY: 1AN XY: 649522
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | The c.1108C>T (p.P370S) alteration is located in exon 7 (coding exon 6) of the PCED1A gene. This alteration results from a C to T substitution at nucleotide position 1108, causing the proline (P) at amino acid position 370 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.