rs11764107

chr7-87892550-G-Achr7-87892550-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
DBF4	NM_006716.4	c.598-3924G>A		intron_variant		ENST00000265728.6
DBF4	NM_001318060.2	c.6-3924G>A		intron_variant
DBF4	NM_001318061.2	c.-75-3924G>A		intron_variant
DBF4	NM_001318062.2	c.-122-3924G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DBF4	ENST00000265728.6	c.598-3924G>A		intron_variant		1	NM_006716.4	P1

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

Gnomad4 AFR AF: 0.00970

Gnomad4 AMR AF: 0.0473

Gnomad4 ASJ AF: 0.0726

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0624

Gnomad4 FIN AF: 0.0149

Gnomad4 NFE AF: 0.0552

Gnomad4 OTH AF: 0.0442

Alfa AF: 0.0480 Hom.: 93

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

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: rs11764107; hg19: chr7-87521865;