rs1370005

Positions:

• chr8-103432781-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015420.7(DCAF13):​c.785+40T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 1,234,872 control chromosomes in the GnomAD database, including 33,924 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.23 (4001 hom., cov: 33)
  • Exomes 𝑓: 0.23 (29923 hom.)
• Consequence: DCAF13 NM_015420.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCAF13	NM_015420.7	c.785+40T>G		intron_variant		ENST00000612750.5
DCAF13	NM_001416065.1	c.440+40T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCAF13	ENST00000612750.5	c.785+40T>G		intron_variant		1	NM_015420.7	P1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34330 AN: 151964 Hom.: 3991 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.229

GnomAD3 exomes AF: 0.236 AC: 56464 AN: 238926 Hom.: 6826 AF XY: 0.237 AC XY: 30747 AN XY: 130006

Gnomad AFR exome AF: 0.213

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: 0.269

Gnomad NFE exome AF: 0.222

Gnomad OTH exome AF: 0.232

GnomAD4 exome AF: 0.233 AC: 251938 AN: 1082788 Hom.: 29923 Cov.: 14 AF XY: 0.233 AC XY: 129756 AN XY: 556166

Gnomad4 AFR exome AF: 0.208

Gnomad4 AMR exome AF: 0.237

Gnomad4 ASJ exome AF: 0.177

Gnomad4 EAS exome AF: 0.363

Gnomad4 SAS exome AF: 0.247

Gnomad4 FIN exome AF: 0.260

Gnomad4 NFE exome AF: 0.227

Gnomad4 OTH exome AF: 0.223

GnomAD4 genome AF: 0.226 AC: 34365 AN: 152084 Hom.: 4001 Cov.: 33 AF XY: 0.231 AC XY: 17133 AN XY: 74328

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.228

Alfa AF: 0.211 Hom.: 837

Bravo AF: 0.223

Asia WGS AF: 0.307 AC: 1065 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	14
DANN	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs1370005; hg19: chr8-104445009;