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GeneBe

rs2383207

Variant summary

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

The NR_003529.3(CDKN2B-AS1):n.2908+2161A>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 0.642 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
NR_003529.3 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.28
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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 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+2161A>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.439-11143A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.642
AC:
97507
AN:
151916
Hom.:
33427
Cov.:
31
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.898
Gnomad4 AMR
AF:
0.611
Gnomad4 ASJ
AF:
0.676
Gnomad4 EAS
AF:
0.670
Gnomad4 SAS
AF:
0.623
Gnomad4 FIN
AF:
0.432
Gnomad4 NFE
AF:
0.524
Gnomad4 OTH
AF:
0.659
Alfa
AF:
0.551
Hom.:
53463
Bravo
AF:
0.664
Asia WGS
AF:
0.639
AC:
2220
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
Cadd
Benign
0.072
Dann
Benign
0.22

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