rs4977575

Positions:

• chr9-22124745-C-G
• chr9-22124745-C-T

Variant summary

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

The NR_185859.1(CDKN2B-AS1):​n.781-2358C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,068 control chromosomes in the GnomAD database, including 32,271 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 0.63 (32271 hom., cov: 32)
• Consequence: CDKN2B-AS1 NR_185859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512

Genes affected

CDKN2B-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2B-AS1	NR_185859.1	n.781-2358C>G		intron_variant
CDKN2B-AS1	NR_185867.1	n.1256-2358C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000650946.1	n.439-2358C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95351 AN: 151950 Hom.: 32214 Cov.: 32

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.628 AC: 95465 AN: 152068 Hom.: 32271 Cov.: 32 AF XY: 0.620 AC XY: 46097 AN XY: 74326

Gnomad4 AFR AF: 0.897

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.642

Alfa AF: 0.372 Hom.: 842

Bravo AF: 0.649

Asia WGS AF: 0.642 AC: 2232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4977575; hg19: chr9-22124744; COSMIC: COSV69592475;