rs1370005

Variant names:

• chr8-103432781-T-G
• rs1370005
• NM_015420.7:c.785+40T>G

Variant summary

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

The NM_015420.7(DCAF13):​c.785+40T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 1,234,872 control chromosomes in the GnomAD database, including 33,924 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 (4001 hom., cov: 33)
  • Exomes 𝑓: 0.23 (29923 hom.)
• Consequence: DCAF13 NM_015420.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 9 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 (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCAF13	NM_015420.7	c.785+40T>G		intron_variant	Intron 7 of 10	ENST00000612750.5	NP_056235.5
DCAF13	NM_001416065.1	c.440+40T>G		intron_variant	Intron 5 of 8		NP_001402994.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCAF13	ENST00000612750.5	c.785+40T>G		intron_variant	Intron 7 of 10	1	NM_015420.7	ENSP00000484962.1
ENSG00000285982	ENST00000649416.1	c.2-24997A>C		intron_variant	Intron 3 of 8			ENSP00000496817.1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34330 AN: 151964 Hom.: 3991 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.229

GnomAD2 exomes AF: 0.236 AC: 56464 AN: 238926 AF XY: 0.237

Gnomad AFR exome AF: 0.213

Gnomad AMR exome AF: 0.235

Gnomad ASJ exome AF: 0.181

Gnomad EAS exome AF: 0.329

Gnomad FIN exome AF: 0.269

Gnomad NFE exome AF: 0.222

Gnomad OTH exome AF: 0.232

GnomAD4 exome AF: 0.233 AC: 251938 AN: 1082788 Hom.: 29923 Cov.: 14 AF XY: 0.233 AC XY: 129756 AN XY: 556166

African (AFR) AF: 0.208 AC: 5301 AN: 25546

American (AMR) AF: 0.237 AC: 10240 AN: 43242

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 4152 AN: 23508

East Asian (EAS) AF: 0.363 AC: 13675 AN: 37722

South Asian (SAS) AF: 0.247 AC: 19268 AN: 77948

European-Finnish (FIN) AF: 0.260 AC: 12287 AN: 47282

Middle Eastern (MID) AF: 0.165 AC: 777 AN: 4712

European-Non Finnish (NFE) AF: 0.227 AC: 175571 AN: 775084

Other (OTH) AF: 0.223 AC: 10667 AN: 47744

GnomAD4 genome AF: 0.226 AC: 34365 AN: 152084 Hom.: 4001 Cov.: 33 AF XY: 0.231 AC XY: 17133 AN XY: 74328

African (AFR) AF: 0.211 AC: 8777 AN: 41528

American (AMR) AF: 0.236 AC: 3600 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3464

East Asian (EAS) AF: 0.342 AC: 1772 AN: 5174

South Asian (SAS) AF: 0.240 AC: 1154 AN: 4816

European-Finnish (FIN) AF: 0.276 AC: 2923 AN: 10572

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

European-Non Finnish (NFE) AF: 0.218 AC: 14816 AN: 67940

Other (OTH) AF: 0.228 AC: 483 AN: 2114

Alfa AF: 0.211 Hom.: 1351

Bravo AF: 0.223

Asia WGS AF: 0.307 AC: 1065 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	14
DANN	Benign	0.72
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1370005; hg19: chr8-104445009;