9-22081797-A-G

Position:

• chr9-22081797-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.2449-14575A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,286 control chromosomes in the GnomAD database, including 3,127 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 0.17 (3127 hom., cov: 33)
• Consequence: CDKN2B-AS1 ENST00000428597.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55

Genes affected

CDKN2B-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.2449-14575A>G		intron_variant
CDKN2B-AS1	NR_047532.2	n.1076-10511A>G		intron_variant
CDKN2B-AS1	NR_047534.2	n.645-15461A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000428597.6	n.2449-14575A>G		intron_variant		1
CDKN2B-AS1	ENST00000577551.5	n.534-30523A>G		intron_variant		1
CDKN2B-AS1	ENST00000580576.6	n.1076-10511A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26573 AN: 152168 Hom.: 3124 Cov.: 33

Gnomad AFR AF: 0.0418

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.175 AC: 26585 AN: 152286 Hom.: 3127 Cov.: 33 AF XY: 0.181 AC XY: 13445 AN XY: 74466

Gnomad4 AFR AF: 0.0417

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.183

Alfa AF: 0.222 Hom.: 1721

Bravo AF: 0.184

Asia WGS AF: 0.155 AC: 539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10965227; hg19: chr9-22081796;