9-22028802-A-G

Position:

• chr9-22028802-A-G

Variant summary

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

The NR_003529.4(CDKN2B-AS1):​n.372-631A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,930 control chromosomes in the GnomAD database, including 26,689 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 0.58 (26689 hom., cov: 32)
• Consequence: CDKN2B-AS1 NR_003529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328

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 (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.372-631A>G		intron_variant
CDKN2B-AS1	NR_047532.2	n.372-631A>G		intron_variant
CDKN2B-AS1	NR_047533.2	n.372-17949A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000428597.6	n.372-631A>G		intron_variant		1
CDKN2B-AS1	ENST00000455933.7	n.341-17949A>G		intron_variant		1
CDKN2B-AS1	ENST00000577551.5	n.261-17949A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88294 AN: 151812 Hom.: 26663 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.582 AC: 88371 AN: 151930 Hom.: 26689 Cov.: 32 AF XY: 0.584 AC XY: 43355 AN XY: 74262

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.602

Alfa AF: 0.511 Hom.: 32679

Bravo AF: 0.602

Asia WGS AF: 0.656 AC: 2275 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.87

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7049105; hg19: chr9-22028801;