Variant 4-145081748-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_001256706.2(ANAPC10):c.118T>G(p.Phe40Val) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,458,496 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

ANAPC10
NM_001256706.2 missense, splice_region

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 8.64

Variant links:

Genes affected

ANAPC10 (HGNC:24077): (anaphase promoting complex subunit 10) ANAPC10 is a core subunit of the anaphase-promoting complex (APC), or cyclosome, a ubiquitin protein ligase that is essential for progression through the cell cycle. APC initiates sister chromatid separation by ubiquitinating the anaphase inhibitor securin (PTTG1; MIM 604147) and triggers exit from mitosis by ubiquitinating cyclin B (CCNB1; MIM 123836), the activating subunit of cyclin-dependent kinase-1 (CDK1; MIM 116940) (summary by Wendt et al., 2001 [PubMed 11524682]).[supplied by OMIM, Feb 2011]

ANAPC10 links:

ENSG00000285713 (HGNC:):

ENSG00000285713 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PP3

MetaRNN computational evidence supports a deleterious effect, 0.772

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANAPC10	NM_001256706.2 linkuse as main transcript	c.118T>G	p.Phe40Val	missense_variant, splice_region_variant	3/5	ENST00000507656.6	NP_001243635.1	Q9UM13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANAPC10	ENST00000507656.6 linkuse as main transcript	c.118T>G	p.Phe40Val	missense_variant, splice_region_variant	3/5	1	NM_001256706.2	ENSP00000423995.1		Q9UM13
ENSG00000285713	ENST00000649263.1 linkuse as main transcript	n.118T>G		splice_region_variant, non_coding_transcript_exon_variant	3/9			ENSP00000497507.1		A0A3B3ISY7

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000804

AC:

AN:

248816

Hom.:

AF XY:

0.00

AC XY:

AN XY:

134990

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000112

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000206

AC:

AN:

1458496

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

725512

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000506

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.0000166

GnomAD4 genome

Cov.:

ExAC

AF:

0.0000166

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 22, 2023

The c.118T>G (p.F40V) alteration is located in exon 3 (coding exon 2) of the ANAPC10 gene. This alteration results from a T to G substitution at nucleotide position 118, causing the phenylalanine (F) at amino acid position 40 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

1.0

BayesDel_addAF

Uncertain

0.041

BayesDel_noAF

Uncertain

0.050

CADD

Pathogenic

DANN

Uncertain

0.98

DEOGEN2

Benign

0.28

T;T;T;T;.;.;.;T;T

Eigen

Pathogenic

0.77

Eigen_PC

Pathogenic

0.73

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Pathogenic

0.98

D;.;.;.;.;D;D;D;D

M_CAP

Benign

0.084

MetaRNN

Pathogenic

0.77

D;D;D;D;D;D;D;D;D

MetaSVM

Benign

-0.52

MutationAssessor

Pathogenic

2.9

M;M;M;M;.;.;.;.;.

PrimateAI

Pathogenic

0.84

PROVEAN

Pathogenic

-4.4

.;D;D;D;D;D;D;D;D

REVEL

Uncertain

0.53

Sift

Benign

0.065

.;T;T;T;T;T;T;T;T

Sift4G

Benign

0.48

T;T;T;T;.;.;T;T;.

Polyphen

0.99

D;D;D;D;.;.;.;.;.

Vest4

0.85

MutPred

0.63

Gain of ubiquitination at K37 (P = 0.0798);Gain of ubiquitination at K37 (P = 0.0798);Gain of ubiquitination at K37 (P = 0.0798);Gain of ubiquitination at K37 (P = 0.0798);Gain of ubiquitination at K37 (P = 0.0798);Gain of ubiquitination at K37 (P = 0.0798);Gain of ubiquitination at K37 (P = 0.0798);Gain of ubiquitination at K37 (P = 0.0798);Gain of ubiquitination at K37 (P = 0.0798);

MVP

0.84

MPC

1.2

ClinPred

0.95

GERP RS

5.4

Varity_R

0.75

gMVP

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over