rs72936240
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Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 8P and 2B. PVS1BP6_Moderate
The NM_022662.4(ANAPC1):c.1393C>T(p.Gln465Ter) variant causes a stop gained change. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.082 ( 0 hom., cov: 33)
Exomes 𝑓: 0.28 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ANAPC1
NM_022662.4 stop_gained
NM_022662.4 stop_gained
Scores
4
2
1
Clinical Significance
Conservation
PhyloP100: 6.60
Genes affected
ANAPC1 (HGNC:19988): (anaphase promoting complex subunit 1) This gene encodes a subunit of the anaphase-promoting complex. This complex is an E3 ubiquitin ligase that regulates progression through the metaphase to anaphase portion of the cell cycle by ubiquitinating proteins which targets them for degradation. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
BP6
?
Variant 2-111856852-G-A is Benign according to our data. Variant chr2-111856852-G-A is described in ClinVar as [Benign]. Clinvar id is 402367.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANAPC1 | NM_022662.4 | c.1393C>T | p.Gln465Ter | stop_gained | 12/48 | ENST00000341068.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANAPC1 | ENST00000341068.8 | c.1393C>T | p.Gln465Ter | stop_gained | 12/48 | 1 | NM_022662.4 | P1 | |
ANAPC1 | ENST00000482177.1 | n.214C>T | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
ANAPC1 | ENST00000427997.5 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0816 AC: 6366AN: 78002Hom.: 0 Cov.: 33
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.282 AC: 272953AN: 967794Hom.: 0 Cov.: 53 AF XY: 0.277 AC XY: 134170AN XY: 484398
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Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0816 AC: 6368AN: 78084Hom.: 0 Cov.: 33 AF XY: 0.0849 AC XY: 3287AN XY: 38726
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ExAC frequency - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
P
Vest4
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 34
Find out detailed SpliceAI scores and Pangolin per-transcript scores at