rs2513993
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032299.4(DCUN1D5):c.341+501T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,008 control chromosomes in the GnomAD database, including 8,612 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 0.32 ( 8612 hom., cov: 32)
Consequence
DCUN1D5
NM_032299.4 intron
NM_032299.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.15
Genes affected
DCUN1D5 (HGNC:28409): (defective in cullin neddylation 1 domain containing 5) Enables cullin family protein binding activity. Involved in cellular response to DNA damage stimulus; positive regulation of protein neddylation; and regulation of cell growth. Located in nucleus and spindle. [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=-0.92).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCUN1D5 | NM_032299.4 | c.341+501T>C | intron_variant | ENST00000260247.10 | |||
DCUN1D5 | NM_001318739.2 | c.134+501T>C | intron_variant | ||||
DCUN1D5 | NM_001318740.2 | c.2+1009T>C | intron_variant | ||||
DCUN1D5 | NM_001318741.2 | c.2+1009T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCUN1D5 | ENST00000260247.10 | c.341+501T>C | intron_variant | 1 | NM_032299.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.319 AC: 48422AN: 151890Hom.: 8599 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.319 AC: 48467AN: 152008Hom.: 8612 Cov.: 32 AF XY: 0.316 AC XY: 23483AN XY: 74298
GnomAD4 genome
?
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152008
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32
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23483
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74298
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1008
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3474
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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