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
NR_003529 intron, non_coding_transcript
Scores
2
Clinical Significance
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-AS1 | NR_003529.3 | 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 | n.439-28528A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.405 AC: 61532AN: 151950Hom.: 13962 Cov.: 32
GnomAD3 genomes
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61532
AN:
151950
Hom.:
Cov.:
32
Gnomad AFR
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Asia WGS
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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:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at