rs2383207

Positions:

• chr9-22115960-A-G
• chr9-22115960-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422420.2(CDKN2B-AS1):​n.134+2161A>G variant causes a intron 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 ENST00000422420.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28

Genes affected

CDKN2B-AS1 (HGNC:):

ACMG classification

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	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.2908+2161A>G		intron_variant
CDKN2B-AS1	NR_047532.2	n.1697+2161A>G		intron_variant
CDKN2B-AS1	NR_047534.2	n.961+2161A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000422420.2	n.134+2161A>G		intron_variant		1
CDKN2B-AS1	ENST00000428597.6	n.2908+2161A>G		intron_variant		1
CDKN2B-AS1	ENST00000577551.5	n.610-2684A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97507 AN: 151916 Hom.: 33427 Cov.: 31

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

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

Other links and lift over

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