rs1265564
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015267.4(CUX2):c.301+6815A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,440 control chromosomes in the GnomAD database, including 9,219 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 0.30 ( 9219 hom., cov: 30)
Exomes 𝑓: 0.25 ( 0 hom. )
Consequence
CUX2
NM_015267.4 intron
NM_015267.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.960
Genes affected
CUX2 (HGNC:19347): (cut like homeobox 2) This gene encodes a protein which contains three CUT domains and a homeodomain; both domains are DNA-binding motifs. A similar gene, whose gene product possesses different DNA-binding activities, is located on chromosome on chromosome 7. Two pseudogenes of this gene have been identified on chromosomes 10 and 4. [provided by RefSeq, Jan 2013]
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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=-0.75).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CUX2 | NM_015267.4 | c.301+6815A>C | intron_variant | ENST00000261726.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CUX2 | ENST00000261726.11 | c.301+6815A>C | intron_variant | 1 | NM_015267.4 | P1 | |||
CUX2 | ENST00000397643.3 | c.481+6815A>C | intron_variant | 1 | |||||
CUX2 | ENST00000551604.2 | n.562A>C | non_coding_transcript_exon_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.299 AC: 45251AN: 151310Hom.: 9221 Cov.: 30
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GnomAD4 exome AF: 0.250 AC: 2AN: 8Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 2AN XY: 8
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GnomAD4 genome ? AF: 0.299 AC: 45237AN: 151432Hom.: 9219 Cov.: 30 AF XY: 0.289 AC XY: 21375AN XY: 73908
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ClinVar
Not reported inComputational scores
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Name
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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