NM_015420.7:c.786-1158C>T

Variant names:

• chr8-103434468-C-T
• rs3098224
• NM_015420.7:c.786-1158C>T

Variant summary

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

The NM_015420.7(DCAF13):​c.786-1158C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,020 control chromosomes in the GnomAD database, including 3,961 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 (3961 hom., cov: 32)
• Consequence: DCAF13 NM_015420.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015420.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCAF13	NM_015420.7	MANE Select	c.786-1158C>T		intron	N/A	NP_056235.5
	DCAF13	NM_001416065.1		c.441-1158C>T		intron	N/A	NP_001402994.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCAF13	ENST00000612750.5	TSL:1 MANE Select	c.786-1158C>T		intron	N/A	ENSP00000484962.1	Q9NV06-1
	DCAF13	ENST00000297579.9	TSL:1	c.1242-1158C>T		intron	N/A	ENSP00000297579.5	A0A087WT20
	DCAF13	ENST00000616836.4	TSL:1	c.1242-1158C>T		intron	N/A	ENSP00000477526.1	A0A087WT20

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34185 AN: 151902 Hom.: 3952 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.225 AC: 34219 AN: 152020 Hom.: 3961 Cov.: 32 AF XY: 0.230 AC XY: 17068 AN XY: 74328

African (AFR) AF: 0.208 AC: 8639 AN: 41498

American (AMR) AF: 0.236 AC: 3594 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 609 AN: 3466

East Asian (EAS) AF: 0.342 AC: 1774 AN: 5182

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4822

European-Finnish (FIN) AF: 0.276 AC: 2927 AN: 10596

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14808 AN: 67882

Other (OTH) AF: 0.227 AC: 478 AN: 2110

Alfa AF: 0.219 Hom.: 1935

Bravo AF: 0.222

Asia WGS AF: 0.305 AC: 1060 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.11
DANN	Benign	0.48
PhyloP100		-2.5
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: rs3098224; hg19: chr8-104446696;