rs94499
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015261.3(NCAPD3):c.4253-470T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 186,584 control chromosomes in the GnomAD database, including 5,499 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 0.24 ( 4677 hom., cov: 32)
Exomes 𝑓: 0.20 ( 822 hom. )
Consequence
NCAPD3
NM_015261.3 intron
NM_015261.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.643
Genes affected
NCAPD3 (HGNC:28952): (non-SMC condensin II complex subunit D3) Condensin complexes I and II play essential roles in mitotic chromosome assembly and segregation. Both condensins contain 2 invariant structural maintenance of chromosome (SMC) subunits, SMC2 (MIM 605576) and SMC4 (MIM 605575), but they contain different sets of non-SMC subunits. NCAPD3 is 1 of 3 non-SMC subunits that define condensin II (Ono et al., 2003 [PubMed 14532007]).[supplied by OMIM, Mar 2008]
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCAPD3 | NM_015261.3 | c.4253-470T>C | intron_variant | ENST00000534548.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCAPD3 | ENST00000534548.7 | c.4253-470T>C | intron_variant | 1 | NM_015261.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.245 AC: 37146AN: 151900Hom.: 4670 Cov.: 32
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GnomAD4 exome AF: 0.198 AC: 6845AN: 34566Hom.: 822 Cov.: 0 AF XY: 0.198 AC XY: 3546AN XY: 17906
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GnomAD4 genome ? AF: 0.245 AC: 37182AN: 152018Hom.: 4677 Cov.: 32 AF XY: 0.245 AC XY: 18223AN XY: 74294
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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