rs1537375
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000422420.2(CDKN2B-AS1):n.134+2273T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 152,046 control chromosomes in the GnomAD database, including 25,465 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 0.57 ( 25465 hom., cov: 32)
Consequence
CDKN2B-AS1
ENST00000422420.2 intron
ENST00000422420.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.135
Genes affected
Genome browser will be placed here
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
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDKN2B-AS1 | NR_003529.4 | n.2908+2273T>C | intron_variant | |||||
CDKN2B-AS1 | NR_047532.2 | n.1697+2273T>C | intron_variant | |||||
CDKN2B-AS1 | NR_047534.2 | n.961+2273T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDKN2B-AS1 | ENST00000422420.2 | n.134+2273T>C | intron_variant | 1 | ||||||
CDKN2B-AS1 | ENST00000428597.6 | n.2908+2273T>C | intron_variant | 1 | ||||||
CDKN2B-AS1 | ENST00000577551.5 | n.610-2572T>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.573 AC: 86998AN: 151928Hom.: 25444 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.573 AC: 87076AN: 152046Hom.: 25465 Cov.: 32 AF XY: 0.566 AC XY: 42066AN XY: 74318
GnomAD4 genome
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32
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42066
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2128
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at