chr11-122091791-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_137178.1(MIR100HG):n.473+8583T>C 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 0.343 in 152,018 control chromosomes in the GnomAD database, including 8,932 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 0.34 ( 8931 hom., cov: 32)
Exomes 𝑓: 0.75 ( 1 hom. )
Consequence
MIR100HG
NR_137178.1 intron, non_coding_transcript
NR_137178.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.284
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=-0.67).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIR100HG | NR_137178.1 | n.473+8583T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIR100HG | ENST00000524376.2 | n.76-72T>C | intron_variant, non_coding_transcript_variant | 1 | |||||
MIR100HG | ENST00000528986.2 | n.897-51T>C | intron_variant, non_coding_transcript_variant | 1 | |||||
MIR100HG | ENST00000534782.4 | n.388-72T>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.343 AC: 52110AN: 151896Hom.: 8925 Cov.: 32
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GnomAD4 exome AF: 0.750 AC: 3AN: 4Hom.: 1 AF XY: 1.00 AC XY: 2AN XY: 2
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GnomAD4 genome ? AF: 0.343 AC: 52149AN: 152014Hom.: 8931 Cov.: 32 AF XY: 0.340 AC XY: 25281AN XY: 74314
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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