rs10517073
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_013367.3(ANAPC4):c.1901+209G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 462,584 control chromosomes in the GnomAD database, including 76,620 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 0.57 ( 25051 hom., cov: 32)
Exomes 𝑓: 0.57 ( 51569 hom. )
Consequence
ANAPC4
NM_013367.3 intron
NM_013367.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.197
Genes affected
ANAPC4 (HGNC:19990): (anaphase promoting complex subunit 4) A large protein complex, termed the anaphase-promoting complex (APC), or the cyclosome, promotes metaphase-anaphase transition by ubiquitinating its specific substrates such as mitotic cyclins and anaphase inhibitor, which are subsequently degraded by the 26S proteasome. Biochemical studies have shown that the vertebrate APC contains eight subunits. The composition of the APC is highly conserved in organisms from yeast to humans. The exact function of this gene product is not known. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 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=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANAPC4 | NM_013367.3 | c.1901+209G>A | intron_variant | ENST00000315368.8 | |||
ANAPC4 | NM_001286756.2 | c.1904+209G>A | intron_variant | ||||
ANAPC4 | XM_005248159.2 | c.800+209G>A | intron_variant | ||||
ANAPC4 | XM_011513838.2 | c.1568+209G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANAPC4 | ENST00000315368.8 | c.1901+209G>A | intron_variant | 1 | NM_013367.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.571 AC: 86675AN: 151864Hom.: 25037 Cov.: 32
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GnomAD4 exome AF: 0.571 AC: 177461AN: 310602Hom.: 51569 Cov.: 4 AF XY: 0.567 AC XY: 91543AN XY: 161576
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GnomAD4 genome AF: 0.571 AC: 86741AN: 151982Hom.: 25051 Cov.: 32 AF XY: 0.571 AC XY: 42431AN XY: 74280
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at