9-22068075-G-A

Position:

• chr9-22068075-G-A

Variant summary

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

The NR_003529.4(CDKN2B-AS1):​n.2448+1722G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0389 in 152,158 control chromosomes in the GnomAD database, including 309 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 0.039 (309 hom., cov: 32)
• Consequence: CDKN2B-AS1 NR_003529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

Genes affected

CDKN2B-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.2448+1722G>A		intron_variant
CDKN2B-AS1	NR_047532.2	n.1075+11688G>A		intron_variant
CDKN2B-AS1	NR_047533.2	n.645-9604G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000428597.6	n.2448+1722G>A		intron_variant		1
CDKN2B-AS1	ENST00000455933.7	n.750-9604G>A		intron_variant		1
CDKN2B-AS1	ENST00000577551.5	n.533+18847G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0388 AC: 5906 AN: 152040 Hom.: 308 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0214

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.00698

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00678

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0389 AC: 5918 AN: 152158 Hom.: 309 Cov.: 32 AF XY: 0.0381 AC XY: 2838 AN XY: 74396

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0214

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0122

Gnomad4 FIN AF: 0.00698

Gnomad4 NFE AF: 0.00678

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0140 Hom.: 47

Bravo AF: 0.0426

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16905597; hg19: chr9-22068074;