chr8-103424650-C-T

Position:

• chr8-103424650-C-T

Variant summary

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

The NM_015420.7(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 NM_015420.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593

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 (NFE) allele frequency at 95% confidence interval = 0.0766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCAF13	NM_015420.7	c.379-1406C>T		intron_variant		ENST00000612750.5
DCAF13	NM_001416065.1	c.34-1406C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCAF13	ENST00000612750.5	c.379-1406C>T		intron_variant		1	NM_015420.7	P1

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

Gnomad4 AFR AF: 0.0201

Gnomad4 AMR AF: 0.0512

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.00694

Gnomad4 SAS AF: 0.0151

Gnomad4 FIN AF: 0.0483

Gnomad4 NFE AF: 0.0783

Gnomad4 OTH AF: 0.0654

Alfa AF: 0.0257 Hom.: 15

Bravo AF: 0.0517

Asia WGS AF: 0.0140 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.81
DANN	Benign	0.58

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: rs3134260; hg19: chr8-104436878;