Variant 17-81900058-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate

The ENST00000344877.10(ANAPC11):c.248A>G(p.Lys83Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,460,318 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0000021 ( 1 hom. )

Consequence

ANAPC11
ENST00000344877.10 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.87

Variant links:

Genes affected

ANAPC11 (HGNC:14452): (anaphase promoting complex subunit 11) Enables cullin family protein binding activity and ubiquitin-ubiquitin ligase activity. Contributes to ubiquitin-protein transferase activity. Involved in protein K11-linked ubiquitination. Located in nucleolus and nucleoplasm. Part of anaphase-promoting complex. [provided by Alliance of Genome Resources, Apr 2022]

ANAPC11 links:

ANAPC11 (HGNC:):

ANAPC11 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.08170399).

BP6

Variant 17-81900058-A-G is Benign according to our data. Variant chr17-81900058-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3293811.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANAPC11	NM_001002248.3 linkuse as main transcript	c.248A>G	p.Lys83Arg	missense_variant	4/4	ENST00000344877.10	NP_001002248.1	Q9NYG5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANAPC11	ENST00000344877.10 linkuse as main transcript	c.248A>G	p.Lys83Arg	missense_variant	4/4	1	NM_001002248.3	ENSP00000339695.5		Q9NYG5-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000205

AC:

AN:

1460318

Hom.:

Cov.:

AF XY:

0.00000413

AC XY:

AN XY:

726384

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000270

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 01, 2024

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.069

BayesDel_addAF

Uncertain

0.14

BayesDel_noAF

Uncertain

-0.040

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.021

T;T;T;T;T;T;T;T;T;T;T;T;T

Eigen

Benign

-0.062

Eigen_PC

Benign

0.10

FATHMM_MKL

Uncertain

0.85

LIST_S2

Benign

0.80

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

M_CAP

Benign

0.020

MetaRNN

Benign

0.082

T;T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.90

MutationTaster

Benign

0.54

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

PROVEAN

Benign

-0.73

.;.;.;N;.;.;.;.;.;.;N;.;.

REVEL

Benign

0.055

Sift

Benign

0.27

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

Sift4G

Benign

0.25

T;T;T;T;T;T;T;T;T;T;T;T;T

Polyphen

0.0060

B;B;B;B;B;B;B;B;B;B;B;B;B

Vest4

0.11

MutPred

0.35

Loss of methylation at K83 (P = 0.0011);Loss of methylation at K83 (P = 0.0011);Loss of methylation at K83 (P = 0.0011);Loss of methylation at K83 (P = 0.0011);Loss of methylation at K83 (P = 0.0011);Loss of methylation at K83 (P = 0.0011);Loss of methylation at K83 (P = 0.0011);Loss of methylation at K83 (P = 0.0011);Loss of methylation at K83 (P = 0.0011);Loss of methylation at K83 (P = 0.0011);Loss of methylation at K83 (P = 0.0011);Loss of methylation at K83 (P = 0.0011);Loss of methylation at K83 (P = 0.0011);

MVP

0.44

ClinPred

0.47

GERP RS

5.2

Varity_R

0.26

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over