rs13238458

Positions:

• chr7-87881104-G-A
• chr7-87881104-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.219+2879G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0454 in 152,204 control chromosomes in the GnomAD database, including 223 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 0.045 (223 hom., cov: 33)
• Consequence: DBF4 NM_006716.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DBF4	NM_006716.4	c.219+2879G>A		intron_variant		ENST00000265728.6
DBF4	NM_001318060.2	c.-374+2879G>A		intron_variant
DBF4	NM_001318061.2	c.-454+2971G>A		intron_variant
DBF4	NM_001318062.2	c.-501+2879G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DBF4	ENST00000265728.6	c.219+2879G>A		intron_variant		1	NM_006716.4	P1

Frequencies

GnomAD3 genomes AF: 0.0455 AC: 6916 AN: 152086 Hom.: 222 Cov.: 33

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0497

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.0715

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0652

Gnomad OTH AF: 0.0650

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

GnomAD4 genome AF: 0.0454 AC: 6912 AN: 152204 Hom.: 223 Cov.: 33 AF XY: 0.0445 AC XY: 3311 AN XY: 74430

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0496

Gnomad4 ASJ AF: 0.0712

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0135

Gnomad4 FIN AF: 0.0715

Gnomad4 NFE AF: 0.0652

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0459 Hom.: 37

Bravo AF: 0.0430

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.78

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: rs13238458; hg19: chr7-87510419;