9-22103814-A-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The ENST00000428597.6(CDKN2B-AS1):n.2698+6450A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,988 control chromosomes in the GnomAD database, including 32,190 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 ( 32190 hom., cov: 31)
Consequence
CDKN2B-AS1
ENST00000428597.6 intron
ENST00000428597.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0830
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=-0.83).
BP6
Variant 9-22103814-A-G is Benign according to our data. Variant chr9-22103814-A-G is described in ClinVar as [protective]. Clinvar id is 812641.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 = 0.885 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.2698+6450A>G | intron_variant | Intron 14 of 18 | 1 | |||||
| CDKN2B-AS1 | ENST00000577551.5 | n.534-8506A>G | intron_variant | Intron 3 of 6 | 1 | |||||
| CDKN2B-AS1 | ENST00000580576.6 | n.1487+6450A>G | intron_variant | Intron 9 of 13 | 1 |
Frequencies
GnomAD3 genomes 0.627 AC: 95233AN: 151870Hom.: 32144 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.627 AC: 95337AN: 151988Hom.: 32190 Cov.: 31 AF XY: 0.619 AC XY: 45926AN XY: 74248
GnomAD4 genome
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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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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at