Variant rs564398 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_003529.3(CDKN2B-AS1):n.487T>C 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 0.28 in 151930 control chromosomes in the gnomAD Genomes database, including 7700 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 0.28 ( 7700 hom., cov: 32)

Exomes 𝑓: 0.31 ( 14061 hom. )

Consequence

CDKN2B-AS1
NR_003529.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.156

Links

CDKN2B-AS1 (HGNC:34341):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDKN2B-AS1	NR_003529.3 linkuse as main transcript	n.487T>C		non_coding_transcript_exon_variant	2/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDKN2B-AS1	ENST00000650946.1 linkuse as main transcript	n.30-17203T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

42493

AN:

151930

Hom.:

7700

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0730

Gnomad AMI

AF:

0.446

Gnomad AMR

AF:

0.212

Gnomad ASJ

AF:

0.282

Gnomad EAS

AF:

0.107

Gnomad SAS

AF:

0.249

Gnomad FIN

AF:

0.411

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.414

Gnomad OTH

AF:

0.263

GnomAD3 exomes

AF:

0.310

AC:

75443

AN:

243314

Hom.:

14061

AF XY:

0.317

AC XY:

42322

AN XY:

133386

show subpopulations

Gnomad AFR exome

AF:

0.0628

Gnomad AMR exome

AF:

0.162

Gnomad ASJ exome

AF:

0.284

Gnomad EAS exome

AF:

0.112

Gnomad SAS exome

AF:

0.257

Gnomad FIN exome

AF:

0.416

Gnomad NFE exome

AF:

0.416

Gnomad OTH exome

AF:

0.327

GnomAD4 exome

AF:

0.343

AC:

214932

AN:

626590

Hom.:

40876

AF XY:

0.341

AC XY:

116419

AN XY:

341414

show subpopulations

Gnomad4 AFR exome

AF:

0.0697

Gnomad4 AMR exome

AF:

0.169

Gnomad4 ASJ exome

AF:

0.284

Gnomad4 EAS exome

AF:

0.134

Gnomad4 SAS exome

AF:

0.256

Gnomad4 FIN exome

AF:

0.414

Gnomad4 NFE exome

AF:

0.413

Gnomad4 OTH exome

AF:

0.330

Alfa

AF:

0.373

Hom.:

22400

Bravo

AF:

0.257

Asia WGS

AF:

0.204

AC:

713

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

Cadd

Benign

6.4

Dann

Benign

0.76

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over