rs13238458

Variant names:

• chr7-87881104-G-A
• rs13238458
• NM_006716.4:c.219+2879G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-87881104-G-A
• chr7-87881104-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0636 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006716.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DBF4	NM_006716.4	MANE Select	c.219+2879G>A		intron	N/A	NP_006707.1
	DBF4	NM_001318061.2		c.-454+2971G>A		intron	N/A	NP_001304990.1
	DBF4	NM_001318060.2		c.-374+2879G>A		intron	N/A	NP_001304989.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DBF4	ENST00000265728.6	TSL:1 MANE Select	c.219+2879G>A		intron	N/A	ENSP00000265728.1
	DBF4	ENST00000413643.5	TSL:1	n.219+2879G>A		intron	N/A	ENSP00000414083.1
	DBF4	ENST00000431138.5	TSL:1	n.127+2971G>A		intron	N/A	ENSP00000407116.1

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

African (AFR) AF: 0.0112 AC: 467 AN: 41538

American (AMR) AF: 0.0496 AC: 758 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 247 AN: 3470

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5174

South Asian (SAS) AF: 0.0135 AC: 65 AN: 4824

European-Finnish (FIN) AF: 0.0715 AC: 758 AN: 10596

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0652 AC: 4431 AN: 68000

Other (OTH) AF: 0.0634 AC: 134 AN: 2114

Alfa AF: 0.0468 Hom.: 70

Bravo AF: 0.0430

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.78
PhyloP100		0.21
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: rs13238458; hg19: chr7-87510419;