rs3134297

chr8-103415350-T-C

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

The ENST00000297579.9(DCAF13):c.360T>C(p.Ser120=) 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.148

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]

ACMG classification

Verdict is Benign. Variant got -15 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_single_submitter, 1 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	HGVSp	Effect	#exon/exons	MANE	UniProt
DCAF13	NM_015420.7			upstream_gene_variant		ENST00000612750.5
DCAF13	NM_001416065.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCAF13	ENST00000612750.5			upstream_gene_variant		1	NM_015420.7	P1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34346 AN: 151698 Hom.: 3995 Cov.: 32

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

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.: 36 AF XY: 0.227 AC XY: 164965 AN XY: 727194

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.: 32 AF XY: 0.231 AC XY: 17144 AN XY: 74186

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:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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	13
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3134297; hg19: chr8-104427578; COSMIC: COSV52567602; COSMIC: COSV52567602;