rs2891168

Positions:

• chr9-22098620-A-G

Variant summary

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

The ENST00000428597.6(CDKN2B-AS1):​n.2698+1256A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 152,066 control chromosomes in the GnomAD database, including 14,116 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 0.41 (14116 hom., cov: 32)
• Consequence: CDKN2B-AS1 ENST00000428597.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442

Genes affected

CDKN2B-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.2698+1256A>G		intron_variant
CDKN2B-AS1	NR_047532.2	n.1487+1256A>G		intron_variant
CDKN2B-AS1	NR_047534.2	n.751+1256A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000428597.6	n.2698+1256A>G		intron_variant		1
CDKN2B-AS1	ENST00000577551.5	n.534-13700A>G		intron_variant		1
CDKN2B-AS1	ENST00000580576.6	n.1487+1256A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62341 AN: 151948 Hom.: 14129 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.410 AC: 62343 AN: 152066 Hom.: 14116 Cov.: 32 AF XY: 0.407 AC XY: 30283 AN XY: 74350

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.476

Alfa AF: 0.483 Hom.: 19702

Bravo AF: 0.400

Asia WGS AF: 0.492 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.42
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2891168; hg19: chr9-22098619;