Variant chr11-122152219-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000534782.4(MIR100HG):n.387+28117G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 534,108 control chromosomes in the GnomAD database, including 28,618 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 0.32 ( 7956 hom., cov: 32)

Exomes 𝑓: 0.32 ( 20662 hom. )

Consequence

MIR100HG
ENST00000534782.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.05

Variant links:

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]

MIR100HG links:

MIR100 (HGNC:31487): (microRNA 100) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR100 links:

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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=-0.74).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
MIR100HG	NR_024430.2 link	n.491+3332G>A	intron_variant
MIR100HG	NR_137179.1 link	n.445+3332G>A	intron_variant
MIR100HG	NR_137180.1 link	n.503+3332G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
MIR100HG	ENST00000534782.4 link	n.387+28117G>A	intron_variant	1
MIR100HG	ENST00000534297.2 link	n.185+3332G>A	intron_variant	4
MIR100HG	ENST00000637700.1 link	n.681+3332G>A	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.318

AC:

48369

AN:

151924

Hom.:

7950

Cov.:

show subpopulations

Gnomad AFR

AF:

0.369

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.324

Gnomad EAS

AF:

0.411

Gnomad SAS

AF:

0.448

Gnomad FIN

AF:

0.230

Gnomad MID

AF:

0.331

Gnomad NFE

AF:

0.298

Gnomad OTH

AF:

0.311

GnomAD3 exomes

AF:

0.316

AC:

79150

AN:

250372

Hom.:

13122

AF XY:

0.323

AC XY:

43822

AN XY:

135512

show subpopulations

Gnomad AFR exome

AF:

0.365

Gnomad AMR exome

AF:

0.256

Gnomad ASJ exome

AF:

0.342

Gnomad EAS exome

AF:

0.393

Gnomad SAS exome

AF:

0.441

Gnomad FIN exome

AF:

0.234

Gnomad NFE exome

AF:

0.294

Gnomad OTH exome

AF:

0.315

GnomAD4 exome

AF:

0.319

AC:

121881

AN:

382066

Hom.:

20662

Cov.:

AF XY:

0.331

AC XY:

72009

AN XY:

217504

show subpopulations

Gnomad4 AFR exome

AF:

0.368

Gnomad4 AMR exome

AF:

0.260

Gnomad4 ASJ exome

AF:

0.339

Gnomad4 EAS exome

AF:

0.399

Gnomad4 SAS exome

AF:

0.443

Gnomad4 FIN exome

AF:

0.237

Gnomad4 NFE exome

AF:

0.292

Gnomad4 OTH exome

AF:

0.312

GnomAD4 genome

AF:

0.318

AC:

48404

AN:

152042

Hom.:

7956

Cov.:

AF XY:

0.317

AC XY:

23597

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.369

Gnomad4 AMR

AF:

0.267

Gnomad4 ASJ

AF:

0.324

Gnomad4 EAS

AF:

0.410

Gnomad4 SAS

AF:

0.448

Gnomad4 FIN

AF:

0.230

Gnomad4 NFE

AF:

0.298

Gnomad4 OTH

AF:

0.309

Alfa

AF:

0.314

Hom.:

2658

Bravo

AF:

0.319

Asia WGS

AF:

0.413

AC:

1436

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Benign

0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over