rs4977574

chr9-22098575-A-Gchr9-22098575-A-T

Variant summary

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

The NR_003529(CDKN2B-AS1):n.2698+1211A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151950 control chromosomes in the gnomAD Genomes database, including 13962 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

Frequency

Genomes: 𝑓 0.40 ( 13962 hom., cov: 32)

Consequence

CDKN2B-AS1
NR_003529 intron, non_coding_transcript

Scores

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: -0.0800

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=-0.74).

BA1

GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.508 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.2698+1211A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDKN2B-AS1	ENST00000650946.1 linkuse as main transcript	n.439-28528A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.405

AC:

61532

AN:

151950

Hom.:

13962

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.495

Gnomad AMR

AF:

0.451

Gnomad ASJ

AF:

0.623

Gnomad EAS

AF:

0.485

Gnomad SAS

AF:

0.525

Gnomad FIN

AF:

0.433

Gnomad MID

AF:

0.642

Gnomad NFE

AF:

0.496

Gnomad OTH

AF:

0.475

Alfa

AF:

0.486

Hom.:

42102

Bravo

AF:

0.394

Asia WGS

AF:

0.490

AC:

1705

AN:

3478

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Three Vessel Coronary Disease

Other:1

risk factor, no assertion criteria provided

clinical testing

Department of Cardiology, Chinese Academy of Medical Sciences, Fuwai Hospital

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

Cadd

Benign

4.8

Dann

Benign

0.92

Splicing

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over