chr9-22088095-A-G

Position:

• chr9-22088095-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.2449-8277A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,508 control chromosomes in the GnomAD database, including 14,836 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 0.43 (14836 hom., cov: 31)
• Consequence: CDKN2B-AS1 ENST00000428597.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877

Genes affected

CDKN2B-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.2449-8277A>G		intron_variant
CDKN2B-AS1	NR_047532.2	n.1076-4213A>G		intron_variant
CDKN2B-AS1	NR_047534.2	n.645-9163A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000428597.6	n.2449-8277A>G		intron_variant		1
CDKN2B-AS1	ENST00000577551.5	n.534-24225A>G		intron_variant		1
CDKN2B-AS1	ENST00000580576.6	n.1076-4213A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64419 AN: 151390 Hom.: 14852 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.425 AC: 64425 AN: 151508 Hom.: 14836 Cov.: 31 AF XY: 0.422 AC XY: 31236 AN XY: 74018

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.484

Alfa AF: 0.447 Hom.: 4995

Bravo AF: 0.420

Asia WGS AF: 0.571 AC: 1985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.87
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10738607; hg19: chr9-22088094;