rs1365032
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_033830.1(MIR2052HG):n.131+27925C>T 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 0.443 in 151,980 control chromosomes in the GnomAD database, including 15,398 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 0.44 ( 15398 hom., cov: 33)
Consequence
MIR2052HG
NR_033830.1 intron, non_coding_transcript
NR_033830.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.805
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=-0.69).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIR2052HG | NR_033830.1 | n.131+27925C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIR2052HG | ENST00000523442.5 | n.216+27925C>T | intron_variant, non_coding_transcript_variant | 4 | |||||
MIR2052HG | ENST00000518190.4 | n.379+15524C>T | intron_variant, non_coding_transcript_variant | 4 | |||||
MIR2052HG | ENST00000523118.5 | n.131+27925C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.444 AC: 67368AN: 151860Hom.: 15394 Cov.: 33
GnomAD3 genomes
?
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.443 AC: 67396AN: 151980Hom.: 15398 Cov.: 33 AF XY: 0.436 AC XY: 32364AN XY: 74268
GnomAD4 genome
?
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67396
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151980
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33
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32364
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74268
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1691
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3478
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