rs16905613

Positions:

• chr9-22080364-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000428597.6(CDKN2B-AS1):​n.2448+14011A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00877 in 152,340 control chromosomes in the GnomAD database, including 18 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 0.0088 (18 hom., cov: 33)
• Consequence: CDKN2B-AS1 ENST00000428597.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

Genes affected

CDKN2B-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BS2: High Homozygotes in GnomAd4 at 18 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.2448+14011A>G		intron_variant
CDKN2B-AS1	NR_047532.2	n.1076-11944A>G		intron_variant
CDKN2B-AS1	NR_047534.2	n.645-16894A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000428597.6	n.2448+14011A>G		intron_variant		1
CDKN2B-AS1	ENST00000577551.5	n.533+31136A>G		intron_variant		1
CDKN2B-AS1	ENST00000580576.6	n.1076-11944A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.00878 AC: 1336 AN: 152222 Hom.: 18 Cov.: 33

Gnomad AFR AF: 0.00205

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.00190

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00248

Gnomad FIN AF: 0.0296

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.00430

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

GnomAD4 genome AF: 0.00877 AC: 1336 AN: 152340 Hom.: 18 Cov.: 33 AF XY: 0.00924 AC XY: 688 AN XY: 74498

Gnomad4 AFR AF: 0.00204

Gnomad4 AMR AF: 0.00189

Gnomad4 ASJ AF: 0.0231

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00249

Gnomad4 FIN AF: 0.0296

Gnomad4 NFE AF: 0.0112

Gnomad4 OTH AF: 0.00425

Alfa AF: 0.0140 Hom.: 6

Bravo AF: 0.00611

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	8.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16905613; hg19: chr9-22080363;