Genetic Variant CDKN2B-AS1:n.2234-4G>C (chr9-22065658-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000428597.7(CDKN2B-AS1):n.2234-4G>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 151,996 control chromosomes in the GnomAD database, including 32,458 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 0.65 ( 32457 hom., cov: 30)

Exomes 𝑓: 0.67 ( 1 hom. )

Consequence

CDKN2B-AS1
ENST00000428597.7 splice_region, intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.168

Publications

22 publications found

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]

CDKN2B-AS1 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
CDKN2B-AS1	NR_003529.4	MANE Select	n.2234-4G>C	splice_region intron	N/A
CDKN2B-AS1	NR_047532.2		n.1075+9271G>C	intron	N/A
CDKN2B-AS1	NR_047533.2		n.645-12021G>C	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
CDKN2B-AS1	ENST00000428597.7	TSL:1 MANE Select	n.2234-4G>C	splice_region intron	N/A
CDKN2B-AS1	ENST00000455933.8	TSL:1	n.749+9271G>C	intron	N/A
CDKN2B-AS1	ENST00000577551.5	TSL:1	n.533+16430G>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.651

AC:

98824

AN:

151872

Hom.:

32437

Cov.:

show subpopulations

Gnomad AFR

AF:

0.659

Gnomad AMI

AF:

0.559

Gnomad AMR

AF:

0.758

Gnomad ASJ

AF:

0.752

Gnomad EAS

AF:

0.783

Gnomad SAS

AF:

0.759

Gnomad FIN

AF:

0.617

Gnomad MID

AF:

0.794

Gnomad NFE

AF:

0.604

Gnomad OTH

AF:

0.676

GnomAD4 exome

AF:

0.667

AC:

AN:

Hom.:

Cov.:

AF XY:

0.667

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.651

AC:

98884

AN:

151990

Hom.:

32457

Cov.:

AF XY:

0.653

AC XY:

48508

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.658

AC:

27285

AN:

41446

American (AMR)

AF:

0.758

AC:

11586

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.752

AC:

2608

AN:

3466

East Asian (EAS)

AF:

0.784

AC:

4047

AN:

5164

South Asian (SAS)

AF:

0.760

AC:

3654

AN:

4810

European-Finnish (FIN)

AF:

0.617

AC:

6509

AN:

10552

Middle Eastern (MID)

AF:

0.799

AC:

235

AN:

294

European-Non Finnish (NFE)

AF:

0.604

AC:

41034

AN:

67952

Other (OTH)

AF:

0.671

AC:

1418

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1728

3457

5185

6914

8642

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

804

1608

2412

3216

4020

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.612

Hom.:

3385

Bravo

AF:

0.659

Asia WGS

AF:

0.721

AC:

2506

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

7.1

(source)

DANN

Benign

0.63

PhyloP100

0.17

Mutation Taster

=10/90

disease causing (long InDel)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over