Variant 9-22010576-G-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+15415G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00901 in 152,230 control chromosomes in the GnomAD database, including 111 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 ( 111 hom., cov: 33)

Consequence

CDKN2B-AS1
ENST00000428597.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.476

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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
CDKN2B-AS1	NR_003529.4 linkuse as main transcript	n.371+15415G>A	intron_variant
CDKN2B-AS1	NR_047532.2 linkuse as main transcript	n.371+15415G>A	intron_variant
CDKN2B-AS1	NR_047533.2 linkuse as main transcript	n.371+15415G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
CDKN2B-AS1	ENST00000428597.6 linkuse as main transcript	n.371+15415G>A	intron_variant	1
CDKN2B-AS1	ENST00000455933.7 linkuse as main transcript	n.340+15415G>A	intron_variant	1
CDKN2B-AS1	ENST00000577551.5 linkuse as main transcript	n.260+15415G>A	intron_variant	1

Frequencies

GnomAD3 genomes

AF:

0.00901

AC:

1371

AN:

152112

Hom.:

111

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000411

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00151

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.194

Gnomad SAS

AF:

0.0602

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:

0.00901

AC:

1371

AN:

152230

Hom.:

111

Cov.:

AF XY:

0.0105

AC XY:

779

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.000409

Gnomad4 AMR

AF:

0.00150

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.194

Gnomad4 SAS

AF:

0.0605

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000353

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.000484

Hom.:

Bravo

AF:

0.00884

Asia WGS

AF:

0.0850

AC:

296

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.82

DANN

Benign

0.54

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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