Variant rs11558511 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001198956.2(DCAF6):c.1871T>C(p.Val624Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 1,609,918 control chromosomes in the GnomAD database, including 58,387 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.21 ( 3963 hom., cov: 32)

Exomes 𝑓: 0.27 ( 54424 hom. )

Consequence

DCAF6
NM_001198956.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0670

Variant links:

Genes affected

DCAF6 (HGNC:30002): (DDB1 and CUL4 associated factor 6) The protein encoded by this gene is a ligand-dependent coactivator of nuclear receptors, including nuclear receptor subfamily 3 group C member 1 (NR3C1), glucocorticoid receptor (GR), and androgen receptor (AR). The encoded protein and DNA damage binding protein 2 (DDB2) may act as tumor promoters and tumor suppressors, respectively, by regulating the level of androgen receptor in prostate tissues. In addition, this protein can act with glucocorticoid receptor to promote human papillomavirus gene expression. [provided by RefSeq, Mar 2017]

DCAF6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0040177405).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCAF6	NM_001198956.2 link	c.1871T>C	p.Val624Ala	missense_variant	15/22	ENST00000367840.4	NP_001185885.1	Q58WW2-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCAF6	ENST00000367840.4 link	c.1871T>C	p.Val624Ala	missense_variant	15/22	1	NM_001198956.2	ENSP00000356814.3		Q58WW2-3

Frequencies

GnomAD3 genomes

AF:

0.211

AC:

32032

AN:

151970

Hom.:

3964

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0804

Gnomad AMI

AF:

0.284

Gnomad AMR

AF:

0.149

Gnomad ASJ

AF:

0.287

Gnomad EAS

AF:

0.211

Gnomad SAS

AF:

0.265

Gnomad FIN

AF:

0.301

Gnomad MID

AF:

0.175

Gnomad NFE

AF:

0.281

Gnomad OTH

AF:

0.212

GnomAD3 exomes

AF:

0.241

AC:

60452

AN:

250876

Hom.:

7994

AF XY:

0.250

AC XY:

33920

AN XY:

135592

show subpopulations

Gnomad AFR exome

AF:

0.0786

Gnomad AMR exome

AF:

0.112

Gnomad ASJ exome

AF:

0.292

Gnomad EAS exome

AF:

0.195

Gnomad SAS exome

AF:

0.275

Gnomad FIN exome

AF:

0.310

Gnomad NFE exome

AF:

0.283

Gnomad OTH exome

AF:

0.250

GnomAD4 exome

AF:

0.268

AC:

391049

AN:

1457830

Hom.:

54424

Cov.:

AF XY:

0.269

AC XY:

195481

AN XY:

725392

show subpopulations

Gnomad4 AFR exome

AF:

0.0704

Gnomad4 AMR exome

AF:

0.117

Gnomad4 ASJ exome

AF:

0.293

Gnomad4 EAS exome

AF:

0.224

Gnomad4 SAS exome

AF:

0.273

Gnomad4 FIN exome

AF:

0.315

Gnomad4 NFE exome

AF:

0.279

Gnomad4 OTH exome

AF:

0.260

GnomAD4 genome

AF:

0.211

AC:

32028

AN:

152088

Hom.:

3963

Cov.:

AF XY:

0.210

AC XY:

15647

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.0802

Gnomad4 AMR

AF:

0.149

Gnomad4 ASJ

AF:

0.287

Gnomad4 EAS

AF:

0.211

Gnomad4 SAS

AF:

0.265

Gnomad4 FIN

AF:

0.301

Gnomad4 NFE

AF:

0.281

Gnomad4 OTH

AF:

0.210

Alfa

AF:

0.261

Hom.:

11636

Bravo

AF:

0.191

TwinsUK

AF:

0.272

AC:

1010

ALSPAC

AF:

0.273

AC:

1053

ESP6500AA

AF:

0.0869

AC:

383

ESP6500EA

AF:

0.275

AC:

2364

ExAC

AF:

0.246

AC:

29838

Asia WGS

AF:

0.222

AC:

775

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Benign

0.82

DEOGEN2

Benign

0.014

.;.;T;.

Eigen

Benign

-0.87

Eigen_PC

Benign

-0.71

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.57

T;T;T;T

MetaRNN

Benign

0.0040

T;T;T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

1.0

.;.;L;.

PrimateAI

Benign

0.28

PROVEAN

Benign

-0.24

N;N;N;N

REVEL

Benign

0.031

Sift

Benign

0.31

T;T;T;T

Sift4G

Benign

0.83

T;T;T;T

Polyphen

0.0010, 0.0050

.;B;B;B

Vest4

0.081

MPC

0.43

ClinPred

0.0057

GERP RS

2.5

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.0

Varity_R

0.056

gMVP

0.083

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over