rs10495594
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_110196.1(MIR3681HG):n.327+23418G>A 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 0.113 in 151,904 control chromosomes in the GnomAD database, including 1,831 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 0.11 ( 1831 hom., cov: 31)
Consequence
MIR3681HG
NR_110196.1 intron, non_coding_transcript
NR_110196.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.358
Genes affected
MIR3681HG (HGNC:52001): (MIR3681 host gene)
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=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIR3681HG | NR_110196.1 | n.327+23418G>A | intron_variant, non_coding_transcript_variant | ||||
LOC105373432 | XR_922806.2 | n.368-479C>T | intron_variant, non_coding_transcript_variant | ||||
LOC105373432 | XR_922807.2 | n.279-479C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIR3681HG | ENST00000412294.5 | n.315+23418G>A | intron_variant, non_coding_transcript_variant | 2 | |||||
ENST00000701120.1 | n.390-479C>T | intron_variant, non_coding_transcript_variant | |||||||
MIR3681HG | ENST00000438292.5 | n.246+23418G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.113 AC: 17158AN: 151786Hom.: 1823 Cov.: 31
GnomAD3 genomes
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17158
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151786
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.113 AC: 17191AN: 151904Hom.: 1831 Cov.: 31 AF XY: 0.123 AC XY: 9169AN XY: 74244
GnomAD4 genome
?
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17191
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151904
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31
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9169
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74244
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1452
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at