rs13238458
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
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
NM_006716.4 intron
Scores
2
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]
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ACMG classification
Classification made for transcript
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: 6916AN: 152086Hom.: 222 Cov.: 33
GnomAD3 genomes
?
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152086
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0454 AC: 6912AN: 152204Hom.: 223 Cov.: 33 AF XY: 0.0445 AC XY: 3311AN XY: 74430
GnomAD4 genome
?
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AC:
6912
AN:
152204
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33
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3311
AN XY:
74430
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26
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at