rs17009221
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000657366.1(MIR29B2CHG):n.405T>C 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 0.0956 in 518,622 control chromosomes in the GnomAD database, including 2,964 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 0.12 ( 1340 hom., cov: 33)
Exomes 𝑓: 0.085 ( 1624 hom. )
Consequence
MIR29B2CHG
ENST00000657366.1 non_coding_transcript_exon
ENST00000657366.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.374
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=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIR29B2CHG | ENST00000657366.1 | n.405T>C | non_coding_transcript_exon_variant | 3/5 | |||||
MIR29B2CHG | ENST00000435542.3 | n.202+1924T>C | intron_variant, non_coding_transcript_variant | 3 | |||||
MIR29B2CHG | ENST00000637970.1 | n.217+1924T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.120 AC: 18244AN: 152164Hom.: 1336 Cov.: 33
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GnomAD3 exomes AF: 0.0871 AC: 19920AN: 228648Hom.: 1153 AF XY: 0.0870 AC XY: 10996AN XY: 126372
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GnomAD4 exome AF: 0.0854 AC: 31300AN: 366340Hom.: 1624 Cov.: 0 AF XY: 0.0849 AC XY: 17832AN XY: 210020
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GnomAD4 genome ? AF: 0.120 AC: 18258AN: 152282Hom.: 1340 Cov.: 33 AF XY: 0.116 AC XY: 8643AN XY: 74462
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at