rs2898002
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_138371.3(PCED1B):c.-609+2719C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,096 control chromosomes in the GnomAD database, including 6,236 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.27 ( 6236 hom., cov: 32)
Consequence
PCED1B
NM_138371.3 intron
NM_138371.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.37
Genes affected
PCED1B (HGNC:28255): (PC-esterase domain containing 1B) This gene encodes a protein that belongs to the GDSL/SGNH-like acyl-esterase family. Members of this family are hydrolases thought to function in modification of biopolymers on the cell surface. Alternate splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCED1B | NM_138371.3 | c.-609+2719C>G | intron_variant | ENST00000546455.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCED1B | ENST00000546455.6 | c.-609+2719C>G | intron_variant | 1 | NM_138371.3 | P1 | |||
PCED1B | ENST00000432328.2 | c.-141+2719C>G | intron_variant | 3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.274 AC: 41689AN: 151978Hom.: 6229 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.274 AC: 41722AN: 152096Hom.: 6236 Cov.: 32 AF XY: 0.278 AC XY: 20647AN XY: 74332
GnomAD4 genome
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20647
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1195
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3478
ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at