rs1537378

Variant names:

• chr9-22061615-A-G
• rs1537378
• ENST00000428597.7:n.2085-338A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000428597.7(CDKN2B-AS1):​n.2085-338A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,034 control chromosomes in the GnomAD database, including 42,619 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 0.73 (42619 hom., cov: 32)
• Consequence: CDKN2B-AS1 ENST00000428597.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 45 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.2085-338A>G		intron_variant	Intron 8 of 18
CDKN2B-AS1	NR_047532.2	n.1075+5228A>G		intron_variant	Intron 6 of 13
CDKN2B-AS1	NR_047533.2	n.644+12387A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000428597.7	n.2085-338A>G		intron_variant	Intron 8 of 18	1
CDKN2B-AS1	ENST00000455933.8	n.749+5228A>G		intron_variant	Intron 4 of 4	1
CDKN2B-AS1	ENST00000577551.5	n.533+12387A>G		intron_variant	Intron 3 of 6	1

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111622 AN: 151916 Hom.: 42560 Cov.: 32

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.735 AC: 111734 AN: 152034 Hom.: 42619 Cov.: 32 AF XY: 0.735 AC XY: 54592 AN XY: 74278

African (AFR) AF: 0.931 AC: 38678 AN: 41526

American (AMR) AF: 0.796 AC: 12160 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2615 AN: 3470

East Asian (EAS) AF: 0.871 AC: 4505 AN: 5170

South Asian (SAS) AF: 0.766 AC: 3678 AN: 4802

European-Finnish (FIN) AF: 0.622 AC: 6545 AN: 10530

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41233 AN: 67946

Other (OTH) AF: 0.743 AC: 1568 AN: 2110

Alfa AF: 0.646 Hom.: 53551

Bravo AF: 0.756

Asia WGS AF: 0.786 AC: 2706 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.68
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1537378; hg19: chr9-22061614;