rs750606

Positions:

• chr8-103416302-T-C

Variant summary

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

The ENST00000612750.5(DCAF13):​c.70+786T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,178 control chromosomes in the GnomAD database, including 1,780 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 0.14 (1780 hom., cov: 32)
• Consequence: DCAF13 ENST00000612750.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCAF13	NM_015420.7	c.70+786T>C		intron_variant		ENST00000612750.5	NP_056235.5
DCAF13	NM_001416065.1	c.33+786T>C		intron_variant			NP_001402994.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCAF13	ENST00000612750.5	c.70+786T>C		intron_variant		1	NM_015420.7	ENSP00000484962	P1

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21820 AN: 152060 Hom.: 1780 Cov.: 32

Gnomad AFR AF: 0.0885

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.139

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.143 AC: 21817 AN: 152178 Hom.: 1780 Cov.: 32 AF XY: 0.152 AC XY: 11283 AN XY: 74386

Gnomad4 AFR AF: 0.0885

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.140

Alfa AF: 0.144 Hom.: 2200

Bravo AF: 0.137

Asia WGS AF: 0.281 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.75

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

Other links and lift over

dbSNP: rs750606; hg19: chr8-104428530;