8-103424650-C-T

Variant names:

• chr8-103424650-C-T
• rs3134260
• NM_015420.7:c.379-1406C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000612750.5(DCAF13):​c.379-1406C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0521 in 152,280 control chromosomes in the GnomAD database, including 270 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 0.052 (270 hom., cov: 32)
• Consequence: DCAF13 ENST00000612750.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593
• Publications: 1 publications found

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]

ENSG00000285982 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0766 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000612750.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCAF13	NM_015420.7	MANE Select	c.379-1406C>T		intron	N/A	NP_056235.5
	DCAF13	NM_001416065.1		c.34-1406C>T		intron	N/A	NP_001402994.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCAF13	ENST00000612750.5	TSL:1 MANE Select	c.379-1406C>T		intron	N/A	ENSP00000484962.1
	DCAF13	ENST00000297579.9	TSL:1	c.835-1406C>T		intron	N/A	ENSP00000297579.5
	DCAF13	ENST00000616836.4	TSL:1	c.835-1406C>T		intron	N/A	ENSP00000477526.1

Frequencies

GnomAD3 genomes AF: 0.0522 AC: 7941 AN: 152162 Hom.: 270 Cov.: 32

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0512

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.00693

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.0483

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0784

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0521 AC: 7939 AN: 152280 Hom.: 270 Cov.: 32 AF XY: 0.0503 AC XY: 3746 AN XY: 74478

African (AFR) AF: 0.0201 AC: 835 AN: 41560

American (AMR) AF: 0.0512 AC: 783 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3472

East Asian (EAS) AF: 0.00694 AC: 36 AN: 5186

South Asian (SAS) AF: 0.0151 AC: 73 AN: 4826

European-Finnish (FIN) AF: 0.0483 AC: 513 AN: 10614

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0783 AC: 5327 AN: 68004

Other (OTH) AF: 0.0654 AC: 138 AN: 2110

Alfa AF: 0.0262 Hom.: 16

Bravo AF: 0.0517

Asia WGS AF: 0.0140 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.81
DANN	Benign	0.58
PhyloP100		-0.59
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3134260; hg19: chr8-104436878;