Genetic Variant CDKN2B-AS1:n.2448+5949G>C (chr9-22072302-G-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The ENST00000428597.6(CDKN2B-AS1):n.2448+5949G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,130 control chromosomes in the GnomAD database, including 32,625 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as protective (no stars).

Frequency

Genomes: 𝑓 0.63 ( 32625 hom., cov: 33)

Consequence

CDKN2B-AS1
ENST00000428597.6 intron

Scores

Clinical Significance

protective no assertion criteria provided B:1

Conservation

PhyloP100: -0.395

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 made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 9-22072302-G-C is Benign according to our data. Variant chr9-22072302-G-C is described in ClinVar as [protective]. Clinvar id is 812645.Status of the report is no_assertion_criteria_provided, 0 stars. We mark this variant Likely_benign, oryginal submission is: [protective].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
CDKN2B-AS1	NR_003529.4 link	n.2448+5949G>C	intron_variant	Intron 12 of 18
CDKN2B-AS1	NR_047532.2 link	n.1075+15915G>C	intron_variant	Intron 6 of 13
CDKN2B-AS1	NR_047533.2 link	n.645-5377G>C	intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CDKN2B-AS1	ENST00000428597.6 link	n.2448+5949G>C	intron_variant	Intron 12 of 18	1
CDKN2B-AS1	ENST00000455933.7 link	n.750-5377G>C	intron_variant	Intron 4 of 4	1
CDKN2B-AS1	ENST00000577551.5 link	n.533+23074G>C	intron_variant	Intron 3 of 6	1

Frequencies

GnomAD3 genomes

AF:

0.629

AC:

95627

AN:

152012

Hom.:

32579

Cov.:

show subpopulations

Gnomad AFR

AF:

0.906

Gnomad AMI

AF:

0.502

Gnomad AMR

AF:

0.565

Gnomad ASJ

AF:

0.663

Gnomad EAS

AF:

0.709

Gnomad SAS

AF:

0.650

Gnomad FIN

AF:

0.438

Gnomad MID

AF:

0.744

Gnomad NFE

AF:

0.496

Gnomad OTH

AF:

0.648

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

GnomAD4 genome

AF:

0.629

AC:

95733

AN:

152130

Hom.:

32625

Cov.:

AF XY:

0.622

AC XY:

46284

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.906

Gnomad4 AMR

AF:

0.565

Gnomad4 ASJ

AF:

0.663

Gnomad4 EAS

AF:

0.709

Gnomad4 SAS

AF:

0.649

Gnomad4 FIN

AF:

0.438

Gnomad4 NFE

AF:

0.496

Gnomad4 OTH

AF:

0.644

Alfa

AF:

0.400

Hom.:

1065

Bravo

AF:

0.647

Asia WGS

AF:

0.677

AC:

2353

AN:

3478

ClinVar

Significance: protective

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Three Vessel Coronary Disease

Benign:1

Department of Cardiology, Chinese Academy of Medical Sciences, Fuwai Hospital

Significance: protective

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

7.3

DANN

Benign

0.76

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over