Variant 14-24115658-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_025230.5(DCAF11):c.64C>G(p.Arg22Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,638 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

DCAF11
NM_025230.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.06

Variant links:

Genes affected

DCAF11 (HGNC:20258): (DDB1 and CUL4 associated factor 11) This gene encodes a WD repeat-containing protein that interacts with the COP9 signalosome, a macromolecular complex that interacts with cullin-RING E3 ligases and regulates their activity by hydrolyzing cullin-Nedd8 conjugates. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2009]

DCAF11 links:

DCAF11 (HGNC:):

DCAF11 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.18135396).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCAF11	NM_025230.5 linkuse as main transcript	c.64C>G	p.Arg22Gly	missense_variant	2/15	ENST00000446197.8	NP_079506.3	Q8TEB1-1Q59GN6B3KSW2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCAF11	ENST00000446197.8 linkuse as main transcript	c.64C>G	p.Arg22Gly	missense_variant	2/15	1	NM_025230.5	ENSP00000415556.4		Q8TEB1-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000400

AC:

AN:

250074

Hom.:

AF XY:

0.00

AC XY:

AN XY:

135500

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000274

AC:

AN:

1461638

Hom.:

Cov.:

AF XY:

0.00000275

AC XY:

AN XY:

727120

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:

0.0000348

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

8.99e-7

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ExAC

AF:

0.00000824

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

Mar 11, 2022

The c.64C>G (p.R22G) alteration is located in exon 2 (coding exon 1) of the DCAF11 gene. This alteration results from a C to G substitution at nucleotide position 64, causing the arginine (R) at amino acid position 22 to be replaced by a glycine (G). 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

Benign

0.063

BayesDel_addAF

Benign

-0.061

BayesDel_noAF

Benign

-0.23

CADD

Benign

DANN

Benign

0.94

DEOGEN2

Benign

0.0088

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

Eigen

Benign

-0.28

Eigen_PC

Benign

-0.095

FATHMM_MKL

Uncertain

0.79

M_CAP

Benign

0.024

MetaRNN

Benign

0.18

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

MetaSVM

Benign

-0.91

MutationAssessor

Benign

0.34

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

PrimateAI

Uncertain

0.51

PROVEAN

Benign

-1.6

N;N;N;N;N;N;D;N;N;D;N;D;N;N;D;N;N;D;N;N

REVEL

Benign

0.15

Sift

Uncertain

0.010

D;D;D;D;T;D;.;D;D;D;D;.;D;D;D;D;D;D;D;D

Sift4G

Benign

0.15

T;T;T;T;T;T;D;T;T;D;T;D;T;T;D;T;T;D;T;T

Polyphen

0.0040, 0.0060

.;B;.;.;.;B;.;.;.;.;.;.;.;.;.;.;.;.;.;B

Vest4

0.38, 0.24, 0.46

MutPred

0.27

Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);Gain of methylation at R23 (P = 0.0787);

MVP

0.43

MPC

0.50

ClinPred

0.26

GERP RS

3.5

Varity_R

0.11

gMVP

0.11

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

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