Variant chr9-22010005-T-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000428597.6(CDKN2B-AS1):n.371+14844T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,054 control chromosomes in the GnomAD database, including 8,076 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 0.31 ( 8076 hom., cov: 32)

Consequence

CDKN2B-AS1
ENST00000428597.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.230

Variant links:

Genes affected

CDKN2B-AS1 (HGNC:):

CDKN2B-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
CDKN2B-AS1	NR_003529.4 linkuse as main transcript	n.371+14844T>A	intron_variant
CDKN2B-AS1	NR_047532.2 linkuse as main transcript	n.371+14844T>A	intron_variant
CDKN2B-AS1	NR_047533.2 linkuse as main transcript	n.371+14844T>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
CDKN2B-AS1	ENST00000428597.6 linkuse as main transcript	n.371+14844T>A	intron_variant	1
CDKN2B-AS1	ENST00000455933.7 linkuse as main transcript	n.340+14844T>A	intron_variant	1
CDKN2B-AS1	ENST00000577551.5 linkuse as main transcript	n.260+14844T>A	intron_variant	1

Frequencies

GnomAD3 genomes

AF:

0.311

AC:

47319

AN:

151936

Hom.:

8089

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.345

Gnomad AMR

AF:

0.353

Gnomad ASJ

AF:

0.419

Gnomad EAS

AF:

0.581

Gnomad SAS

AF:

0.414

Gnomad FIN

AF:

0.337

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.344

Gnomad OTH

AF:

0.353

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

GnomAD4 genome

AF:

0.311

AC:

47306

AN:

152054

Hom.:

8076

Cov.:

AF XY:

0.314

AC XY:

23335

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.176

Gnomad4 AMR

AF:

0.353

Gnomad4 ASJ

AF:

0.419

Gnomad4 EAS

AF:

0.581

Gnomad4 SAS

AF:

0.414

Gnomad4 FIN

AF:

0.337

Gnomad4 NFE

AF:

0.345

Gnomad4 OTH

AF:

0.349

Alfa

AF:

0.180

Hom.:

379

Bravo

AF:

0.310

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

6.0

DANN

Benign

0.85

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

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over