Variant chr8-103415350-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000297579.9(DCAF13):c.360T>C(p.Ser120Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 1,613,590 control chromosomes in the GnomAD database, including 42,233 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 4005 hom., cov: 32)

Exomes 𝑓: 0.23 ( 38228 hom. )

Consequence

DCAF13
ENST00000297579.9 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.148

Variant links:

Genes affected

DCAF13 (HGNC:24535): (DDB1 and CUL4 associated factor 13) Enables estrogen receptor binding activity. Predicted to be involved in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Located in several cellular components, including centrosome; cytosol; and nuclear lumen. Part of Cul4-RING E3 ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

DCAF13 links:

ENSG00000285982 (HGNC:):

ENSG00000285982 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 8-103415350-T-C is Benign according to our data. Variant chr8-103415350-T-C is described in ClinVar as [Benign]. Clinvar id is 1252673.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.148 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
	use as main transcript	n.103415350T>C	intergenic_region
DCAF13	NM_015420.7 linkuse as main transcript	c.-97T>C	upstream_gene_variant	ENST00000612750.5	NP_056235.5	Q9NV06-1A0A087WT20
DCAF13	NM_001416065.1 linkuse as main transcript	c.-134T>C	upstream_gene_variant		NP_001402994.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285982	ENST00000649416.1 linkuse as main transcript	c.2-7566A>G		intron_variant				ENSP00000496817.1		A0A3B3IRK5
DCAF13	ENST00000612750.5 linkuse as main transcript	c.-97T>C		upstream_gene_variant		1	NM_015420.7	ENSP00000484962.1		Q9NV06-1

Frequencies

GnomAD3 genomes

AF:

0.226

AC:

34346

AN:

151698

Hom.:

3995

Cov.:

show subpopulations

Gnomad AFR

AF:

0.211

Gnomad AMI

AF:

0.201

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.176

Gnomad EAS

AF:

0.343

Gnomad SAS

AF:

0.243

Gnomad FIN

AF:

0.278

Gnomad MID

AF:

0.166

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.230

GnomAD3 exomes

AF:

0.236

AC:

59163

AN:

250596

Hom.:

7238

AF XY:

0.236

AC XY:

32055

AN XY:

135804

show subpopulations

Gnomad AFR exome

AF:

0.212

Gnomad AMR exome

AF:

0.235

Gnomad ASJ exome

AF:

0.181

Gnomad EAS exome

AF:

0.329

Gnomad SAS exome

AF:

0.247

Gnomad FIN exome

AF:

0.266

Gnomad NFE exome

AF:

0.221

Gnomad OTH exome

AF:

0.233

GnomAD4 exome

AF:

0.226

AC:

330644

AN:

1461774

Hom.:

38228

Cov.:

AF XY:

0.227

AC XY:

164965

AN XY:

727194

show subpopulations

Gnomad4 AFR exome

AF:

0.203

Gnomad4 AMR exome

AF:

0.237

Gnomad4 ASJ exome

AF:

0.174

Gnomad4 EAS exome

AF:

0.360

Gnomad4 SAS exome

AF:

0.246

Gnomad4 FIN exome

AF:

0.261

Gnomad4 NFE exome

AF:

0.220

Gnomad4 OTH exome

AF:

0.219

GnomAD4 genome

AF:

0.226

AC:

34381

AN:

151816

Hom.:

4005

Cov.:

AF XY:

0.231

AC XY:

17144

AN XY:

74186

show subpopulations

Gnomad4 AFR

AF:

0.212

Gnomad4 AMR

AF:

0.236

Gnomad4 ASJ

AF:

0.176

Gnomad4 EAS

AF:

0.343

Gnomad4 SAS

AF:

0.242

Gnomad4 FIN

AF:

0.278

Gnomad4 NFE

AF:

0.218

Gnomad4 OTH

AF:

0.229

Alfa

AF:

0.216

Hom.:

2855

Bravo

AF:

0.223

Asia WGS

AF:

0.306

AC:

1064

AN:

3478

EpiCase

AF:

0.219

EpiControl

AF:

0.221

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 14, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

DANN

Benign

0.79

Splicing

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