NM_006716.4:c.598-3924G>A

Variant names:

• chr7-87892550-G-A
• rs11764107
• NM_006716.4:c.598-3924G>A

Variant summary

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

The NM_006716.4(DBF4):​c.598-3924G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0378 in 152,216 control chromosomes in the GnomAD database, including 151 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 0.038 (151 hom., cov: 33)
• Consequence: DBF4 NM_006716.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 7 publications found

Genes affected

DBF4 (HGNC:17364): (DBF4-CDC7 kinase regulatory subunit) Predicted to enable protein serine/threonine kinase activator activity. Predicted to be involved in positive regulation of nuclear cell cycle DNA replication and regulation of cell cycle phase transition. Located in nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DBF4	NM_006716.4	c.598-3924G>A		intron_variant	Intron 6 of 11	ENST00000265728.6	NP_006707.1
DBF4	NM_001318061.2	c.-75-3924G>A		intron_variant	Intron 6 of 11		NP_001304990.1
DBF4	NM_001318060.2	c.6-3924G>A		intron_variant	Intron 6 of 10		NP_001304989.1
DBF4	NM_001318062.2	c.-122-3924G>A		intron_variant	Intron 6 of 11		NP_001304991.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DBF4	ENST00000265728.6	c.598-3924G>A		intron_variant	Intron 6 of 11	1	NM_006716.4	ENSP00000265728.1

Frequencies

GnomAD3 genomes AF: 0.0378 AC: 5756 AN: 152098 Hom.: 152 Cov.: 33

Gnomad AFR AF: 0.00973

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0630

Gnomad FIN AF: 0.0149

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0551

Gnomad OTH AF: 0.0446

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

GnomAD4 genome AF: 0.0378 AC: 5752 AN: 152216 Hom.: 151 Cov.: 33 AF XY: 0.0369 AC XY: 2746 AN XY: 74418

African (AFR) AF: 0.00970 AC: 403 AN: 41532

American (AMR) AF: 0.0473 AC: 724 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0726 AC: 252 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0624 AC: 301 AN: 4822

European-Finnish (FIN) AF: 0.0149 AC: 158 AN: 10584

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0552 AC: 3751 AN: 68014

Other (OTH) AF: 0.0442 AC: 93 AN: 2106

Alfa AF: 0.0491 Hom.: 102

Bravo AF: 0.0386

Asia WGS AF: 0.0270 AC: 95 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.7
DANN	Benign	0.80
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism

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: rs11764107; hg19: chr7-87521865;