Variant chr7-87907873-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_006716.4(DBF4):c.1735A>G(p.Lys579Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0115 in 1,613,642 control chromosomes in the GnomAD database, including 136 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0083 ( 7 hom., cov: 32)

Exomes 𝑓: 0.012 ( 129 hom. )

Consequence

DBF4
NM_006716.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 4.45

Variant links:

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]

DBF4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0038783252).

BP6

Variant 7-87907873-A-G is Benign according to our data. Variant chr7-87907873-A-G is described in ClinVar as [Benign]. Clinvar id is 779253.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
DBF4	NM_006716.4 linkuse as main transcript	c.1735A>G	p.Lys579Glu	missense_variant	12/12	ENST00000265728.6
DBF4	NM_001318061.2 linkuse as main transcript	c.1063A>G	p.Lys355Glu	missense_variant	12/12
DBF4	NM_001318060.2 linkuse as main transcript	c.1036A>G	p.Lys346Glu	missense_variant	11/11
DBF4	NM_001318062.2 linkuse as main transcript	c.955A>G	p.Lys319Glu	missense_variant	12/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DBF4	ENST00000265728.6 linkuse as main transcript	c.1735A>G	p.Lys579Glu	missense_variant	12/12	1	NM_006716.4	P1	Q9UBU7-1
DBF4	ENST00000413643.5 linkuse as main transcript	c.*969A>G		3_prime_UTR_variant, NMD_transcript_variant	12/12	1			Q9UBU7-2
DBF4	ENST00000431138.5 linkuse as main transcript	c.*1508A>G		3_prime_UTR_variant, NMD_transcript_variant	12/12	1

Frequencies

GnomAD3 genomes

AF:

0.00830

AC:

1264

AN:

152244

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00289

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.00850

Gnomad ASJ

AF:

0.00375

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00269

Gnomad FIN

AF:

0.00320

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0136

Gnomad OTH

AF:

0.0105

GnomAD3 exomes

AF:

0.00826

AC:

2055

AN:

248714

Hom.:

AF XY:

0.00835

AC XY:

1127

AN XY:

134930

show subpopulations

Gnomad AFR exome

AF:

0.00286

Gnomad AMR exome

AF:

0.00621

Gnomad ASJ exome

AF:

0.00459

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00336

Gnomad FIN exome

AF:

0.00425

Gnomad NFE exome

AF:

0.0134

Gnomad OTH exome

AF:

0.00875

GnomAD4 exome

AF:

0.0119

AC:

17347

AN:

1461280

Hom.:

129

Cov.:

AF XY:

0.0116

AC XY:

8439

AN XY:

726882

show subpopulations

Gnomad4 AFR exome

AF:

0.00218

Gnomad4 AMR exome

AF:

0.00703

Gnomad4 ASJ exome

AF:

0.00390

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00339

Gnomad4 FIN exome

AF:

0.00345

Gnomad4 NFE exome

AF:

0.0142

Gnomad4 OTH exome

AF:

0.00964

GnomAD4 genome

AF:

0.00830

AC:

1264

AN:

152362

Hom.:

Cov.:

AF XY:

0.00816

AC XY:

608

AN XY:

74506

show subpopulations

Gnomad4 AFR

AF:

0.00289

Gnomad4 AMR

AF:

0.00849

Gnomad4 ASJ

AF:

0.00375

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00290

Gnomad4 FIN

AF:

0.00320

Gnomad4 NFE

AF:

0.0136

Gnomad4 OTH

AF:

0.00994

Alfa

AF:

0.0121

Hom.:

Bravo

AF:

0.00911

TwinsUK

AF:

0.0167

AC:

ALSPAC

AF:

0.0148

AC:

ESP6500AA

AF:

0.00363

AC:

ESP6500EA

AF:

0.0116

AC:

ExAC

AF:

0.00774

AC:

939

EpiCase

AF:

0.0136

EpiControl

AF:

0.0141

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 12, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.33

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.068

Eigen

Benign

0.047

Eigen_PC

Benign

0.18

FATHMM_MKL

Uncertain

0.77

LIST_S2

Benign

0.82

MetaRNN

Benign

0.0039

MetaSVM

Benign

-0.98

MutationAssessor

Uncertain

2.3

MutationTaster

Benign

0.77

PrimateAI

Benign

0.32

PROVEAN

Benign

-0.93

REVEL

Benign

0.059

Sift

Uncertain

0.029

Sift4G

Benign

0.13

Polyphen

0.068

Vest4

0.16

MVP

0.19

MPC

0.30

ClinPred

0.021

GERP RS

4.0

Varity_R

0.14

gMVP

0.24

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over