rs2383208

Variant names:

• chr9-22132077-A-G
• rs2383208
• ENST00000755351.1:n.302+4675A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-22132077-A-G
• chr9-22132077-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000755351.1(CDKN2B-AS1):​n.302+4675A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,054 control chromosomes in the GnomAD database, including 2,764 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 0.18 (2764 hom., cov: 30)
• Consequence: CDKN2B-AS1 ENST00000755351.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 146 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755351.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDKN2B-AS1	ENST00000755351.1		n.302+4675A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27758 AN: 151936 Hom.: 2760 Cov.: 30

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.190

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.183 AC: 27781 AN: 152054 Hom.: 2764 Cov.: 30 AF XY: 0.182 AC XY: 13558 AN XY: 74336

African (AFR) AF: 0.186 AC: 7709 AN: 41470

American (AMR) AF: 0.174 AC: 2664 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 572 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2043 AN: 5154

South Asian (SAS) AF: 0.143 AC: 690 AN: 4816

European-Finnish (FIN) AF: 0.150 AC: 1587 AN: 10574

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11923 AN: 67978

Other (OTH) AF: 0.191 AC: 403 AN: 2110

Alfa AF: 0.182 Hom.: 9506

Bravo AF: 0.187

Asia WGS AF: 0.293 AC: 1018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.50
PhyloP100		-0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2383208;

hg19: chr9-22132076;