chr9-22031006-G-A

Position:

• chr9-22031006-G-A

Variant summary

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

The ENST00000645313.2(CDKN2B-AS1):​n.1913G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,090 control chromosomes in the GnomAD database, including 40,758 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 0.72 (40758 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CDKN2B-AS1 ENST00000645313.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

Genes affected

CDKN2B-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.533+1412G>A		intron_variant
CDKN2B-AS1	NR_047532.2	n.533+1412G>A		intron_variant
CDKN2B-AS1	NR_047533.2	n.372-15745G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000428597.6	n.533+1412G>A		intron_variant		1
CDKN2B-AS1	ENST00000455933.7	n.341-15745G>A		intron_variant		1
CDKN2B-AS1	ENST00000577551.5	n.261-15745G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108664 AN: 151972 Hom.: 40701 Cov.: 32

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.732

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.715 AC: 108774 AN: 152090 Hom.: 40758 Cov.: 32 AF XY: 0.716 AC XY: 53264 AN XY: 74342

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.727

Alfa AF: 0.615 Hom.: 43844

Bravo AF: 0.738

Asia WGS AF: 0.795 AC: 2758 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.5
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7865618; hg19: chr9-22031005;