GeneBe

rs35699984

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_016238.3(ANAPC7):​c.936-15_936-7delTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000046 in 869,406 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: not found (cov: 0)
Exomes 𝑓: 0.0000046 ( 0 hom. )

Consequence

ANAPC7
NM_016238.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.618

Publications

0 publications found
Variant links:
Genes affected
ANAPC7 (HGNC:17380): (anaphase promoting complex subunit 7) This gene encodes a tetratricopeptide repeat containing component of the anaphase promoting complex/cyclosome (APC/C), a large E3 ubiquitin ligase that controls cell cycle progression by targeting a number of cell cycle regulators such as B-type cyclins for 26S proteasome-mediated degradation through ubiquitination. The encoded protein is required for proper protein ubiquitination function of APC/C and for the interaction of APC/C with certain transcription coactivators. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2008]
ANAPC7 Gene-Disease associations (from GenCC):
  • Ferguson-Bonni neurodevelopmental syndrome
    Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016238.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ANAPC7
NM_016238.3
MANE Select
c.936-15_936-7delTTTTTTTTT
splice_region intron
N/ANP_057322.3Q9UJX3-1
ANAPC7
NM_001385208.1
c.978-15_978-7delTTTTTTTTT
splice_region intron
N/ANP_001372137.1
ANAPC7
NM_001137664.2
c.936-15_936-7delTTTTTTTTT
splice_region intron
N/ANP_001131136.2Q9UJX3-2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ANAPC7
ENST00000455511.9
TSL:1 MANE Select
c.936-15_936-7delTTTTTTTTT
splice_region intron
N/AENSP00000394394.4Q9UJX3-1
ANAPC7
ENST00000450008.3
TSL:1
c.936-15_936-7delTTTTTTTTT
splice_region intron
N/AENSP00000402314.3Q9UJX3-2
ANAPC7
ENST00000471602.6
TSL:1
n.424-15_424-7delTTTTTTTTT
splice_region intron
N/A

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000460
AC:
4
AN:
869406
Hom.:
0
AF XY:
0.00000465
AC XY:
2
AN XY:
430334
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
17494
American (AMR)
AF:
0.00
AC:
0
AN:
16632
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
13020
East Asian (EAS)
AF:
0.00
AC:
0
AN:
21756
South Asian (SAS)
AF:
0.00
AC:
0
AN:
46448
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
25102
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2310
European-Non Finnish (NFE)
AF:
0.00000579
AC:
4
AN:
690972
Other (OTH)
AF:
0.00
AC:
0
AN:
35672
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.463
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.62
Mutation Taster
=100/0
polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs35699984; hg19: chr12-110819759; API