9-22118103-T-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000643286.1(CDKN2B-AS1):n.516T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0218 in 152,384 control chromosomes in the GnomAD database, including 153 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 0.022 ( 153 hom., cov: 32)
Exomes 𝑓: 0.010 ( 0 hom. )
Consequence
CDKN2B-AS1
ENST00000643286.1 non_coding_transcript_exon
ENST00000643286.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.205
Genes affected
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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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDKN2B-AS1 | NR_003529.4 | n.2909-541T>G | intron_variant | |||||
CDKN2B-AS1 | NR_047532.2 | n.1698-541T>G | intron_variant | |||||
CDKN2B-AS1 | NR_047534.2 | n.962-541T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDKN2B-AS1 | ENST00000422420.2 | n.135-2097T>G | intron_variant | 1 | ||||||
CDKN2B-AS1 | ENST00000428597.6 | n.2909-541T>G | intron_variant | 1 | ||||||
CDKN2B-AS1 | ENST00000577551.5 | n.610-541T>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0218 AC: 3318AN: 152164Hom.: 153 Cov.: 32
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GnomAD4 exome AF: 0.0100 AC: 1AN: 100Hom.: 0 Cov.: 0 AF XY: 0.0161 AC XY: 1AN XY: 62
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GnomAD4 genome AF: 0.0218 AC: 3322AN: 152284Hom.: 153 Cov.: 32 AF XY: 0.0228 AC XY: 1698AN XY: 74468
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ClinVar
Not reported inComputational scores
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Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at