rs3098218

Variant names:

• chr8-103439971-G-A
• rs3098218
• NM_015420.7:c.951-165G>A

Variant summary

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

The NM_015420.7(DCAF13):​c.951-165G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 449,428 control chromosomes in the GnomAD database, including 55,480 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 0.49 (18586 hom., cov: 32)
  • Exomes 𝑓: 0.49 (36894 hom.)
• Consequence: DCAF13 NM_015420.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.653
• Publications: 11 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCAF13	NM_015420.7	c.951-165G>A		intron_variant	Intron 8 of 10	ENST00000612750.5	NP_056235.5
DCAF13	NM_001416065.1	c.606-165G>A		intron_variant	Intron 6 of 8		NP_001402994.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCAF13	ENST00000612750.5	c.951-165G>A		intron_variant	Intron 8 of 10	1	NM_015420.7	ENSP00000484962.1
ENSG00000285982	ENST00000649416.1	c.2-32187C>T		intron_variant	Intron 3 of 8			ENSP00000496817.1

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74959 AN: 151742 Hom.: 18566 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.511

GnomAD4 exome AF: 0.494 AC: 146973 AN: 297568 Hom.: 36894 Cov.: 5 AF XY: 0.493 AC XY: 74700 AN XY: 151642

African (AFR) AF: 0.504 AC: 3853 AN: 7648

American (AMR) AF: 0.430 AC: 3198 AN: 7432

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 4677 AN: 8874

East Asian (EAS) AF: 0.380 AC: 7953 AN: 20946

South Asian (SAS) AF: 0.397 AC: 2720 AN: 6850

European-Finnish (FIN) AF: 0.517 AC: 10306 AN: 19952

Middle Eastern (MID) AF: 0.486 AC: 634 AN: 1304

European-Non Finnish (NFE) AF: 0.508 AC: 105181 AN: 207000

Other (OTH) AF: 0.481 AC: 8451 AN: 17562

GnomAD4 genome AF: 0.494 AC: 75015 AN: 151860 Hom.: 18586 Cov.: 32 AF XY: 0.494 AC XY: 36640 AN XY: 74204

African (AFR) AF: 0.503 AC: 20813 AN: 41398

American (AMR) AF: 0.454 AC: 6919 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1906 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1834 AN: 5168

South Asian (SAS) AF: 0.396 AC: 1902 AN: 4804

European-Finnish (FIN) AF: 0.525 AC: 5527 AN: 10522

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34421 AN: 67936

Other (OTH) AF: 0.507 AC: 1068 AN: 2106

Alfa AF: 0.499 Hom.: 32730

Bravo AF: 0.486

Asia WGS AF: 0.406 AC: 1410 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.68
PhyloP100		0.65
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: rs3098218; hg19: chr8-104452199;