chr12-8932728-CGCAGCAGCA-C
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The ENST00000544916.6(PHC1):c.1281_1289del(p.Gln437_Gln439del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00000658 in 151,952 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 27)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PHC1
ENST00000544916.6 inframe_deletion
ENST00000544916.6 inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.04
Genes affected
PHC1 (HGNC:3182): (polyhomeotic homolog 1) This gene is a homolog of the Drosophila polyhomeotic gene, which is a member of the Polycomb group of genes. The gene product is a component of a multimeric protein complex that contains EDR2 and the vertebrate Polycomb protein BMH1. The gene product, the EDR2 protein, and the Drosophila polyhomeotic protein share 2 highly conserved domains, named homology domains I and II. These domains are involved in protein-protein interactions and may mediate heterodimerization of the protein encoded by this gene and the EDR2 protein. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in ENST00000544916.6.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PHC1 | NM_004426.3 | c.1281_1289del | p.Gln437_Gln439del | inframe_deletion | 8/15 | ENST00000544916.6 | NP_004417.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| PHC1 | ENST00000544916.6 | c.1281_1289del | p.Gln437_Gln439del | inframe_deletion | 8/15 | 1 | NM_004426.3 | ENSP00000437659 | P1 |
Frequencies
GnomAD3 genomes 0.00000658 AC: 1AN: 151952Hom.: 0 Cov.: 27
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GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248330Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134438
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000205 AC: 3AN: 1461032Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 726798
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome 0.00000658 AC: 1AN: 151952Hom.: 0 Cov.: 27 AF XY: 0.0000135 AC XY: 1AN XY: 74198
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at