rs3848516
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004852.3(ONECUT2):c.*11425A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,530 control chromosomes in the GnomAD database, including 24,003 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 0.52 ( 23910 hom., cov: 33)
Exomes 𝑓: 0.66 ( 93 hom. )
Consequence
ONECUT2
NM_004852.3 3_prime_UTR
NM_004852.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.54
Genes affected
ONECUT2 (HGNC:8139): (one cut homeobox 2) This gene encodes a member of the onecut family of transcription factors, which are characterized by a cut domain and an atypical homeodomain. The protein binds to specific DNA sequences and stimulates expression of target genes, including genes involved in melanocyte and hepatocyte differentiation. [provided by RefSeq, Jul 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=-0.52).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ONECUT2 | NM_004852.3 | c.*11425A>G | 3_prime_UTR_variant | 2/2 | ENST00000491143.3 | ||
ONECUT2 | XM_047437947.1 | c.*11636A>G | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ONECUT2 | ENST00000491143.3 | c.*11425A>G | 3_prime_UTR_variant | 2/2 | 1 | NM_004852.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.522 AC: 79383AN: 151990Hom.: 23921 Cov.: 33
GnomAD3 genomes
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GnomAD4 exome AF: 0.659 AC: 278AN: 422Hom.: 93 Cov.: 0 AF XY: 0.621 AC XY: 159AN XY: 256
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GnomAD4 genome ? AF: 0.522 AC: 79364AN: 152108Hom.: 23910 Cov.: 33 AF XY: 0.517 AC XY: 38413AN XY: 74352
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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