Genetic Variant ANAPC7:c.936-10_936-7dupTTTT (chr12-110381954-G-GAAAA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_016238.3(ANAPC7):c.936-10_936-7dupTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0014 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ANAPC7
NM_016238.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

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)

ANAPC7 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ANAPC7	NM_016238.3	MANE Select	c.936-10_936-7dupTTTT	splice_region intron	N/A	NP_057322.3	Q9UJX3-1
ANAPC7	NM_001385208.1		c.978-10_978-7dupTTTT	splice_region intron	N/A	NP_001372137.1
ANAPC7	NM_001137664.2		c.936-10_936-7dupTTTT	splice_region intron	N/A	NP_001131136.2	Q9UJX3-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ANAPC7	ENST00000455511.9	TSL:1 MANE Select	c.936-7_936-6insTTTT	splice_region intron	N/A	ENSP00000394394.4	Q9UJX3-1
ANAPC7	ENST00000450008.3	TSL:1	c.936-7_936-6insTTTT	splice_region intron	N/A	ENSP00000402314.3	Q9UJX3-2
ANAPC7	ENST00000471602.6	TSL:1	n.424-7_424-6insTTTT	splice_region intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

107702

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00142

AC:

1233

AN:

868488

Hom.:

Cov.:

AF XY:

0.00161

AC XY:

694

AN XY:

429794

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00126

AC:

AN:

17488

American (AMR)

AF:

0.00392

AC:

AN:

16574

Ashkenazi Jewish (ASJ)

AF:

0.00246

AC:

AN:

13008

East Asian (EAS)

AF:

0.00202

AC:

AN:

21730

South Asian (SAS)

AF:

0.00621

AC:

287

AN:

46206

European-Finnish (FIN)

AF:

0.00156

AC:

AN:

25058

Middle Eastern (MID)

AF:

0.00173

AC:

AN:

2308

European-Non Finnish (NFE)

AF:

0.00101

AC:

696

AN:

690486

Other (OTH)

AF:

0.00123

AC:

AN:

35630

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.370

Heterozygous variant carriers

112

167

223

279

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

100

<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

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

107702

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

50812

African (AFR)

AF:

0.00

AC:

AN:

28816

American (AMR)

AF:

0.00

AC:

AN:

10124

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2626

East Asian (EAS)

AF:

0.00

AC:

AN:

3188

South Asian (SAS)

AF:

0.00

AC:

AN:

2944

European-Finnish (FIN)

AF:

0.00

AC:

AN:

4936

Middle Eastern (MID)

AF:

0.00

AC:

AN:

214

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

52700

Other (OTH)

AF:

0.00

AC:

AN:

1430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.0

Splicing

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

Publications

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12-110381954-GAAAAAAAAA-GAAAAAAAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over