9-22088261-C-T

Position:

• chr9-22088261-C-T

Variant summary

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

The NR_003529.4(CDKN2B-AS1):​n.2449-8111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,912 control chromosomes in the GnomAD database, including 14,779 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 0.42 (14779 hom., cov: 32)
• Consequence: CDKN2B-AS1 NR_003529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

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 (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.2449-8111C>T		intron_variant
CDKN2B-AS1	NR_047532.2	n.1076-4047C>T		intron_variant
CDKN2B-AS1	NR_047534.2	n.645-8997C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000428597.6	n.2449-8111C>T		intron_variant		1
CDKN2B-AS1	ENST00000577551.5	n.534-24059C>T		intron_variant		1
CDKN2B-AS1	ENST00000580576.6	n.1076-4047C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63978 AN: 151794 Hom.: 14793 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.421 AC: 63985 AN: 151912 Hom.: 14779 Cov.: 32 AF XY: 0.419 AC XY: 31094 AN XY: 74266

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.478

Alfa AF: 0.490 Hom.: 34523

Bravo AF: 0.413

Asia WGS AF: 0.566 AC: 1967 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	0.58
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10757272; hg19: chr9-22088260;