Genetic Variant CDKN2B-AS1:n.847-2390A>T (chr9-22043927-A-T) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is The variant received 2 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_Moderate

The NR_003529.4(CDKN2B-AS1):n.847-2390A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

CDKN2B-AS1
NR_003529.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.908

Publications

0 publications found

Variant links:

Genes affected

CDKN2B-AS1 (HGNC:34341): (CDKN2B and CDKN2A antisense cis and trans regulatory 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]

CDKN2B-AS1 links:

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new If you want to explore the variant's impact on the transcript NR_003529.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 2 points.

Show applied only (1)

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	O3Absent or very rare in population		Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = absent, AC = 0 — absent/extremely rare (O3 moderate [+2])

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NR_003529.4. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
CDKN2B-AS1 NR_003529.4	MANE Select	n.847-2390A>T	intron	Intron 3 of 18	Prot:
CDKN2B-AS1 NR_047532.2		n.534-2390A>T	intron	Intron 2 of 13	Prot:
CDKN2B-AS1 NR_047533.2		n.372-2824A>T	intron	Intron 1 of 3	Prot:

CDKN2B-AS1 NR_003529.4

MANE Select

HGVSc / HGVSpn.847-2390A>T

Exon rankIntron 3 of 18

intron

Prot:

CDKN2B-AS1 NR_047532.2

HGVSc / HGVSpn.534-2390A>T

Exon rankIntron 2 of 13

intron

Prot:

CDKN2B-AS1 NR_047533.2

HGVSc / HGVSpn.372-2824A>T

Exon rankIntron 1 of 3

intron

Prot:

Ensembl Transcripts

Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
CDKN2B-AS1 ENST00000428597.7	TSL:1MANE Select	n.847-2390A>T	intron	Intron 3 of 18	Prot:
CDKN2B-AS1 ENST00000455933.8	TSL:1	n.341-2824A>T	intron	Intron 1 of 4	Prot:
CDKN2B-AS1 ENST00000577551.5	TSL:1	n.261-2824A>T	intron	Intron 1 of 6	Prot:

CDKN2B-AS1 ENST00000428597.7

TSL:1MANE Select

HGVSc / HGVSpn.847-2390A>T

Exon rankIntron 3 of 18

intron

Prot:

CDKN2B-AS1 ENST00000455933.8

TSL:1

HGVSc / HGVSpn.341-2824A>T

Exon rankIntron 1 of 4

intron

Prot:

CDKN2B-AS1 ENST00000577551.5

TSL:1

HGVSc / HGVSpn.261-2824A>T

Exon rankIntron 1 of 6

intron

Prot:

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 2 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 2 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score
AlphaGenome AVI	Benign	0.30
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.25
DANN	Benign	0.40
GPN-Star LLR	N/A	0.061
GPN-Star score	N/A	-0.061
PhyloP100	Benign	-0.91

Showing 7 of 7 scores

Splicing Scores

No splicing scores have been computed for this variant.

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.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACGS-UK Somatic Oncogenicity v2025

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

MaveDB functional evidence ?

Publications

Other links and lift over

MaveDB functional evidence