9-22082376-A-C

Position:

• chr9-22082376-A-C

Variant summary

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

The ENST00000428597.6(CDKN2B-AS1):​n.2449-13996A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,204 control chromosomes in the GnomAD database, including 1,877 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 0.14 (1877 hom., cov: 32)
• Consequence: CDKN2B-AS1 ENST00000428597.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

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 = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.2449-13996A>C		intron_variant
CDKN2B-AS1	NR_047532.2	n.1076-9932A>C		intron_variant
CDKN2B-AS1	NR_047534.2	n.645-14882A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000428597.6	n.2449-13996A>C		intron_variant		1
CDKN2B-AS1	ENST00000577551.5	n.534-29944A>C		intron_variant		1
CDKN2B-AS1	ENST00000580576.6	n.1076-9932A>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21828 AN: 152086 Hom.: 1876 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0412

Gnomad FIN AF: 0.0687

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.143 AC: 21840 AN: 152204 Hom.: 1877 Cov.: 32 AF XY: 0.137 AC XY: 10178 AN XY: 74416

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0412

Gnomad4 FIN AF: 0.0687

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.149

Alfa AF: 0.121 Hom.: 1764

Bravo AF: 0.156

Asia WGS AF: 0.0320 AC: 113 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	2.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1547705; hg19: chr9-22082375;