9-22097023-C-T

Position:

• chr9-22097023-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.2592-235C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0419 in 152,248 control chromosomes in the GnomAD database, including 306 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 0.042 (306 hom., cov: 32)
• Consequence: CDKN2B-AS1 ENST00000428597.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.880

Genes affected

CDKN2B-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.2592-235C>T		intron_variant
CDKN2B-AS1	NR_047532.2	n.1381-235C>T		intron_variant
CDKN2B-AS1	NR_047534.2	n.645-235C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000428597.6	n.2592-235C>T		intron_variant		1
CDKN2B-AS1	ENST00000577551.5	n.534-15297C>T		intron_variant		1
CDKN2B-AS1	ENST00000580576.6	n.1381-235C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0418 AC: 6354 AN: 152130 Hom.: 302 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.00745

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0419 AC: 6379 AN: 152248 Hom.: 306 Cov.: 32 AF XY: 0.0419 AC XY: 3119 AN XY: 74436

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0307

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0240

Gnomad4 FIN AF: 0.00745

Gnomad4 NFE AF: 0.0102

Gnomad4 OTH AF: 0.0393

Alfa AF: 0.0111 Hom.: 7

Bravo AF: 0.0465

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16905644; hg19: chr9-22097022;