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GeneBe

rs2383206

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_003529.3(CDKN2B-AS1):n.2908+1228A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,922 control chromosomes in the GnomAD database, including 18,894 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 0.50 ( 18894 hom., cov: 32)

Consequence

CDKN2B-AS1
NR_003529.3 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.53
Variant links:
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CDKN2B-AS1NR_003529.3 linkuse as main transcriptn.2908+1228A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CDKN2B-AS1ENST00000650946.1 linkuse as main transcriptn.439-12076A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.496
AC:
75225
AN:
151804
Hom.:
18897
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.424
Gnomad AMI
AF:
0.499
Gnomad AMR
AF:
0.553
Gnomad ASJ
AF:
0.663
Gnomad EAS
AF:
0.490
Gnomad SAS
AF:
0.555
Gnomad FIN
AF:
0.432
Gnomad MID
AF:
0.712
Gnomad NFE
AF:
0.521
Gnomad OTH
AF:
0.560
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.495
AC:
75253
AN:
151922
Hom.:
18894
Cov.:
32
AF XY:
0.491
AC XY:
36427
AN XY:
74222
show subpopulations
Gnomad4 AFR
AF:
0.424
Gnomad4 AMR
AF:
0.553
Gnomad4 ASJ
AF:
0.663
Gnomad4 EAS
AF:
0.490
Gnomad4 SAS
AF:
0.553
Gnomad4 FIN
AF:
0.432
Gnomad4 NFE
AF:
0.521
Gnomad4 OTH
AF:
0.554
Alfa
AF:
0.524
Hom.:
22502
Bravo
AF:
0.497
Asia WGS
AF:
0.520
AC:
1810
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
0.024
Dann
Benign
0.47

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2383206; hg19: chr9-22115026; COSMIC: COSV69592433; API