rs588354
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000534782.4(MIR100HG):n.387+7298C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0552 in 152,156 control chromosomes in the GnomAD database, including 770 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 0.055 ( 770 hom., cov: 33)
Consequence
MIR100HG
ENST00000534782.4 intron
ENST00000534782.4 intron
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0690
Genes affected
MIR100HG (HGNC:39522): (mir-100-let-7a-2-mir-125b-1 cluster host gene) This gene produces long non-coding RNAs that act as regulators of cell proliferation. Alternative promoter usage and splicing results in multiple transcript variants. Some transcript variants may promote growth, while others may act to negatively regulate cell division. [provided by RefSeq, May 2016]
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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=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MIR100HG | ENST00000534782.4 | n.387+7298C>T | intron_variant | Intron 2 of 2 | 1 | |||||
MIR100HG | ENST00000532350.6 | n.387+7298C>T | intron_variant | Intron 2 of 2 | 5 | |||||
MIR100HG | ENST00000533109.6 | n.916+7298C>T | intron_variant | Intron 6 of 6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0551 AC: 8378AN: 152038Hom.: 765 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: 0.0552 AC: 8402AN: 152156Hom.: 770 Cov.: 33 AF XY: 0.0531 AC XY: 3948AN XY: 74386
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at