rs1537371

Positions:

• chr9-22099569-C-A
• chr9-22099569-C-G
• chr9-22099569-C-T

Variant summary

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

The ENST00000428597.6(CDKN2B-AS1):​n.2698+2205C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,894 control chromosomes in the GnomAD database, including 32,138 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 0.63 (32138 hom., cov: 31)
• Consequence: CDKN2B-AS1 ENST00000428597.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.730

Genes affected

CDKN2B-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.2698+2205C>A		intron_variant
CDKN2B-AS1	NR_047532.2	n.1487+2205C>A		intron_variant
CDKN2B-AS1	NR_047534.2	n.751+2205C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000428597.6	n.2698+2205C>A		intron_variant		1
CDKN2B-AS1	ENST00000577551.5	n.534-12751C>A		intron_variant		1
CDKN2B-AS1	ENST00000580576.6	n.1487+2205C>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95141 AN: 151776 Hom.: 32094 Cov.: 31

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.627 AC: 95243 AN: 151894 Hom.: 32138 Cov.: 31 AF XY: 0.618 AC XY: 45881 AN XY: 74210

Gnomad4 AFR AF: 0.893

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.646

Alfa AF: 0.506 Hom.: 4321

Bravo AF: 0.646

Asia WGS AF: 0.635 AC: 2205 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.5
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1537371; hg19: chr9-22099568;