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GeneBe

rs4977574

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

2

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: -0.0800

Links

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-AS1NR_003529.3 linkuse as main transcriptn.2698+1211A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CDKN2B-AS1ENST00000650946.1 linkuse as main transcriptn.439-28528A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.405
AC:
61532
AN:
151950
Hom.:
13962
Cov.:
32
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 providedclinical testingDepartment 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.

Other links and lift over

dbSNP: rs4977574; hg19: chr9-22098574;