11-122152219-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -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

Publications

25 publications found

Variant links:

COSMIC-nc: COSV66115284

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:

MIR10526 (HGNC:54016): (microRNA 10526) 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]

MIR10526 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 was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000534782.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
MIR100HG	NR_024430.2	n.491+3332G>A	intron	N/A
MIR100HG	NR_137179.1	n.445+3332G>A	intron	N/A
MIR100HG	NR_137180.1	n.503+3332G>A	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIR100HG	ENST00000534782.4	TSL:1	n.387+28117G>A	intron	N/A
MIR100HG	ENST00000534297.2	TSL:4	n.185+3332G>A	intron	N/A
MIR100HG	ENST00000637700.1	TSL:5	n.681+3332G>A	intron	N/A

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

GnomAD2 exomes

AF:

0.316

AC:

79150

AN:

250372

AF XY:

0.323

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 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

African (AFR)

AF:

0.368

AC:

3865

AN:

10498

American (AMR)

AF:

0.260

AC:

9414

AN:

36246

Ashkenazi Jewish (ASJ)

AF:

0.339

AC:

3974

AN:

11726

East Asian (EAS)

AF:

0.399

AC:

5257

AN:

13164

South Asian (SAS)

AF:

0.443

AC:

29532

AN:

66690

European-Finnish (FIN)

AF:

0.237

AC:

7644

AN:

32292

Middle Eastern (MID)

AF:

0.334

AC:

952

AN:

2848

European-Non Finnish (NFE)

AF:

0.292

AC:

56029

AN:

191888

Other (OTH)

AF:

0.312

AC:

5214

AN:

16714

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.431

Heterozygous variant carriers

4613

9226

13838

18451

23064

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

580

1160

1740

2320

2900

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.318

AC:

48404

AN:

152042

Hom.:

7956

Cov.:

AF XY:

0.317

AC XY:

23597

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.369

AC:

15310

AN:

41456

American (AMR)

AF:

0.267

AC:

4085

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.324

AC:

1122

AN:

3464

East Asian (EAS)

AF:

0.410

AC:

2117

AN:

5166

South Asian (SAS)

AF:

0.448

AC:

2155

AN:

4812

European-Finnish (FIN)

AF:

0.230

AC:

2434

AN:

10580

Middle Eastern (MID)

AF:

0.332

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.298

AC:

20257

AN:

67974

Other (OTH)

AF:

0.309

AC:

653

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1652

3304

4957

6609

8261

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

494

988

1482

1976

2470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.316

Hom.:

5701

Bravo

AF:

0.319

Asia WGS

AF:

0.413

AC:

1436

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

(source)

DANN

Benign

0.60

PhyloP100

1.1

Mutation Taster

=98/2

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over