chr9-22115960-A-G

Variant names:

• chr9-22115960-A-G
• rs2383207
• ENST00000428597.7:n.2908+2161A>G

Variant summary

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

The ENST00000428597.7(CDKN2B-AS1):​n.2908+2161A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,034 control chromosomes in the GnomAD database, including 33,471 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 0.64 (33471 hom., cov: 31)
• Consequence: CDKN2B-AS1 ENST00000428597.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 236 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428597.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDKN2B-AS1	NR_003529.4	MANE Select	n.2908+2161A>G		intron	N/A
	CDKN2B-AS1	NR_047532.2		n.1697+2161A>G		intron	N/A
	CDKN2B-AS1	NR_047534.2		n.961+2161A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDKN2B-AS1	ENST00000428597.7	TSL:1 MANE Select	n.2908+2161A>G		intron	N/A
	CDKN2B-AS1	ENST00000422420.3	TSL:1	n.299+2161A>G		intron	N/A
	CDKN2B-AS1	ENST00000577551.5	TSL:1	n.610-2684A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97507 AN: 151916 Hom.: 33427 Cov.: 31

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.642 AC: 97608 AN: 152034 Hom.: 33471 Cov.: 31 AF XY: 0.634 AC XY: 47094 AN XY: 74310

African (AFR) AF: 0.898 AC: 37268 AN: 41508

American (AMR) AF: 0.611 AC: 9331 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2345 AN: 3468

East Asian (EAS) AF: 0.670 AC: 3461 AN: 5162

South Asian (SAS) AF: 0.623 AC: 3005 AN: 4820

European-Finnish (FIN) AF: 0.432 AC: 4549 AN: 10542

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35585 AN: 67956

Other (OTH) AF: 0.659 AC: 1392 AN: 2112

Alfa AF: 0.558 Hom.: 112621

Bravo AF: 0.664

Asia WGS AF: 0.639 AC: 2220 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.072
DANN	Benign	0.22
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2383207; hg19: chr9-22115959; COSMIC: COSV69592447;