rs36229158
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000428597.6(CDKN2B-AS1):n.371+15521G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0154 in 152,316 control chromosomes in the GnomAD database, including 28 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 0.015 ( 28 hom., cov: 33)
Consequence
CDKN2B-AS1
ENST00000428597.6 intron
ENST00000428597.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.231
Genes affected
CDKN2B-AS1 (HGNC:34341): (CDKN2B antisense RNA 1) This gene is located within the CDKN2B-CDKN2A gene cluster at chromosome 9p21. The gene product is a functional RNA molecule that interacts with polycomb repressive complex-1 (PRC1) and -2 (PRC2), leading to epigenetic silencing of other genes in this cluster. This region is a significant genetic susceptibility locus for cardiovascular disease, and has also been linked to a number of other pathologies, including several cancers, intracranial aneurysm, type-2 diabetes, periodontitis, Alzheimer's disease, endometriosis, frailty in the elderly, and glaucoma. Multiple alternatively processed transcript variants have been detected, some of which may take the form of circular RNA molecules (PMID:21151960). [provided by RefSeq, May 2014]
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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).
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0154 (2343/152316) while in subpopulation AMR AF= 0.0248 (379/15306). AF 95% confidence interval is 0.0227. There are 28 homozygotes in gnomad4. There are 1120 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 28 gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDKN2B-AS1 | ENST00000428597.6 | n.371+15521G>A | intron_variant | Intron 1 of 18 | 1 | |||||
CDKN2B-AS1 | ENST00000455933.7 | n.340+15521G>A | intron_variant | Intron 1 of 4 | 1 | |||||
CDKN2B-AS1 | ENST00000577551.5 | n.260+15521G>A | intron_variant | Intron 1 of 6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0154 AC: 2343AN: 152198Hom.: 28 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0154 AC: 2343AN: 152316Hom.: 28 Cov.: 33 AF XY: 0.0150 AC XY: 1120AN XY: 74492
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17
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3478
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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at