rs10965219

Positions:

• chr9-22053688-A-G
• chr9-22053688-A-T

Variant summary

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

The ENST00000428597.6(CDKN2B-AS1):​n.1253-2564A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 152,066 control chromosomes in the GnomAD database, including 26,901 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 (26901 hom., cov: 32)
• Consequence: CDKN2B-AS1 ENST00000428597.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

Genes affected

CDKN2B-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.1253-2564A>G		intron_variant
CDKN2B-AS1	NR_047532.2	n.940-2564A>G		intron_variant
CDKN2B-AS1	NR_047533.2	n.644+4460A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000428597.6	n.1253-2564A>G		intron_variant		1
CDKN2B-AS1	ENST00000455933.7	n.614-2564A>G		intron_variant		1
CDKN2B-AS1	ENST00000577551.5	n.533+4460A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88796 AN: 151948 Hom.: 26870 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.584 AC: 88878 AN: 152066 Hom.: 26901 Cov.: 32 AF XY: 0.586 AC XY: 43579 AN XY: 74310

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.611

Alfa AF: 0.492 Hom.: 4258

Bravo AF: 0.605

Asia WGS AF: 0.666 AC: 2314 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10965219; hg19: chr9-22053687;