chr10-32286516-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001272004.3(EPC1):c.1391+178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 701,706 control chromosomes in the GnomAD database, including 11,919 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 0.16 ( 2125 hom., cov: 32)
Exomes 𝑓: 0.18 ( 9794 hom. )
Consequence
EPC1
NM_001272004.3 intron
NM_001272004.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.264
Genes affected
EPC1 (HGNC:19876): (enhancer of polycomb homolog 1) This gene encodes a member of the polycomb group (PcG) family. The encoded protein is a component of the NuA4 histone acetyltransferase complex and can act as both a transcriptional activator and repressor. The encoded protein has been linked to apoptosis, DNA repair, skeletal muscle differentiation, gene silencing, and adult T-cell leukemia/lymphoma. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]
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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=-0.86).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EPC1 | NM_001272004.3 | c.1391+178G>A | intron_variant | ENST00000319778.11 | NP_001258933.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPC1 | ENST00000319778.11 | c.1391+178G>A | intron_variant | 1 | NM_001272004.3 | ENSP00000318559.6 |
Frequencies
GnomAD3 genomes AF: 0.157 AC: 23818AN: 152012Hom.: 2113 Cov.: 32
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GnomAD4 exome AF: 0.178 AC: 97809AN: 549576Hom.: 9794 Cov.: 8 AF XY: 0.182 AC XY: 51071AN XY: 281310
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GnomAD4 genome AF: 0.157 AC: 23854AN: 152130Hom.: 2125 Cov.: 32 AF XY: 0.163 AC XY: 12122AN XY: 74364
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at