rs77706751

Positions:

• chr9-22031442-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.534-1232C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00902 in 152,158 control chromosomes in the GnomAD database, including 106 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 0.0090 (106 hom., cov: 32)
• Consequence: CDKN2B-AS1 ENST00000428597.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

Genes affected

CDKN2B-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2B-AS1	NR_003529.4	n.534-1232C>T		intron_variant
CDKN2B-AS1	NR_047532.2	n.533+1848C>T		intron_variant
CDKN2B-AS1	NR_047533.2	n.372-15309C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2B-AS1	ENST00000428597.6	n.534-1232C>T		intron_variant		1
CDKN2B-AS1	ENST00000455933.7	n.341-15309C>T		intron_variant		1
CDKN2B-AS1	ENST00000577551.5	n.261-15309C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.00902 AC: 1372 AN: 152038 Hom.: 106 Cov.: 32

Gnomad AFR AF: 0.000411

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00177

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000353

Gnomad OTH AF: 0.00335

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

GnomAD4 genome AF: 0.00902 AC: 1372 AN: 152158 Hom.: 106 Cov.: 32 AF XY: 0.0104 AC XY: 773 AN XY: 74386

Gnomad4 AFR AF: 0.000409

Gnomad4 AMR AF: 0.00177

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.0591

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000353

Gnomad4 OTH AF: 0.00426

Alfa AF: 0.00243 Hom.: 4

Bravo AF: 0.00891

Asia WGS AF: 0.0820 AC: 285 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	2.1
DANN	Benign	0.61

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: rs77706751; hg19: chr9-22031441;