15-89384329-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000538734.7(MIR9-3HG):n.38-3102T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,036 control chromosomes in the GnomAD database, including 13,063 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 0.41 ( 13063 hom., cov: 33)
Consequence
MIR9-3HG
ENST00000538734.7 intron
ENST00000538734.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0370
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=-0.83).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIR9-3HG | NR_015411.1 | n.347-3102T>C | intron_variant | |||||
MIR9-3HG | NR_133001.1 | n.1038-3488T>C | intron_variant | |||||
MIR9-3HG | NR_133002.1 | n.336-3488T>C | intron_variant | |||||
MIR9-3HG | NR_133003.1 | n.262-3102T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MIR9-3HG | ENST00000536780.6 | n.1038-3488T>C | intron_variant | 3 | ||||||
MIR9-3HG | ENST00000538734.7 | n.38-3102T>C | intron_variant | 2 | ||||||
MIR9-3HG | ENST00000546186.3 | n.77-3488T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.407 AC: 61817AN: 151916Hom.: 13058 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.407 AC: 61851AN: 152036Hom.: 13063 Cov.: 33 AF XY: 0.411 AC XY: 30503AN XY: 74290
GnomAD4 genome
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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