rs573687

Positions:

• chr9-22011643-G-A

Variant summary

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

The ENST00000428597.6(CDKN2B-AS1):​n.371+16482G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,000 control chromosomes in the GnomAD database, including 6,426 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 0.25 (6426 hom., cov: 32)
• Consequence: CDKN2B-AS1 ENST00000428597.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803

Genes affected

CDKN2B-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.371+16482G>A		intron_variant
CDKN2B-AS1	NR_047532.2	n.371+16482G>A		intron_variant
CDKN2B-AS1	NR_047533.2	n.371+16482G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000428597.6	n.371+16482G>A		intron_variant		1
CDKN2B-AS1	ENST00000455933.7	n.340+16482G>A		intron_variant		1
CDKN2B-AS1	ENST00000577551.5	n.260+16482G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38693 AN: 151882 Hom.: 6419 Cov.: 32

Gnomad AFR AF: 0.0657

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.255 AC: 38701 AN: 152000 Hom.: 6426 Cov.: 32 AF XY: 0.255 AC XY: 18944 AN XY: 74292

Gnomad4 AFR AF: 0.0656

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.242

Alfa AF: 0.336 Hom.: 5729

Bravo AF: 0.230

Asia WGS AF: 0.200 AC: 698 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	8.7
DANN	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs573687; hg19: chr9-22011642;