9-22072302-G-C
Variant names:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The ENST00000428597.6(CDKN2B-AS1):n.2448+5949G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,130 control chromosomes in the GnomAD database, including 32,625 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as protective (no stars).
Frequency
Genomes: 𝑓 0.63 ( 32625 hom., cov: 33)
Consequence
CDKN2B-AS1
ENST00000428597.6 intron
ENST00000428597.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.395
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 -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
Variant 9-22072302-G-C is Benign according to our data. Variant chr9-22072302-G-C is described in ClinVar as [protective]. Clinvar id is 812645.Status of the report is no_assertion_criteria_provided, 0 stars. We mark this variant Likely_benign, oryginal submission is: [protective].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDKN2B-AS1 | ENST00000428597.6 | n.2448+5949G>C | intron_variant | Intron 12 of 18 | 1 | |||||
CDKN2B-AS1 | ENST00000455933.7 | n.750-5377G>C | intron_variant | Intron 4 of 4 | 1 | |||||
CDKN2B-AS1 | ENST00000577551.5 | n.533+23074G>C | intron_variant | Intron 3 of 6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.629 AC: 95627AN: 152012Hom.: 32579 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: 0.629 AC: 95733AN: 152130Hom.: 32625 Cov.: 33 AF XY: 0.622 AC XY: 46284AN XY: 74366
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ClinVar
Significance: protective
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Three Vessel Coronary Disease Benign:1
-
Department of Cardiology, Chinese Academy of Medical Sciences, Fuwai Hospital
Significance: protective
Review Status: no assertion criteria provided
Collection Method: clinical testing
- -
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at