rs45547937

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The NR_171007.1(MIR1-1HG):n.788-179G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: NR_171007.1 is not a MANE Select or MANE Plus Clinical transcript for MIR1-1HG; the reported annotation may differ from that of the MANE-designated reference transcript for this gene. The variant allele was found at a cumulative frequency of 0.232 (AC=84,166) in the gnomAD database across 363,416 control chromosomes, including 10,295 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.337. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 5181 hom., cov: 35)

Exomes 𝑓: 0.21 ( 5114 hom. )

Consequence

MIR1-1HG
NR_171007.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.809

Publications

5 publications found

Variant links:

COSMIC-nc: COSV61525825

Genes affected

MIR1-1HG (HGNC:16159): (MIR1-1 host gene)

MIR1-1HG links:

MIR133A2 (HGNC:31518): (microRNA 133a-2) 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]

MIR133A2 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NR_171007.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript

Our verdict: Benign. The variant received -12 points.

BP4

Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).

BA1

GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.3367 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NR_171007.1. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR1-1HG	NR_171007.1		n.788-179G>A		intron	N/A
	MIR133A2	NR_029676.1		n.-102G>A		upstream_gene	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIR1-1HG	ENST00000624914.4	TSL:1	n.794-179G>A	intron	N/A
MIR1-1HG	ENST00000370523.4	TSL:5	n.244-5634G>A	intron	N/A
MIR1-1HG	ENST00000686477.2		n.793-5634G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38734

AN:

152046

Hom.:

5180

Cov.:

show subpopulations

Gnomad AFR

AF:

0.342

Gnomad AMI

AF:

0.137

Gnomad AMR

AF:

0.257

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.178

Gnomad FIN

AF:

0.187

Gnomad MID

AF:

0.258

Gnomad NFE

AF:

0.229

Gnomad OTH

AF:

0.246

GnomAD4 exome

AF:

0.215

AC:

45409

AN:

211252

Hom.:

5114

AF XY:

0.211

AC XY:

24335

AN XY:

115092

show subpopulations

African (AFR)

AF:

0.343

AC:

1727

AN:

5034

American (AMR)

AF:

0.239

AC:

2419

AN:

10112

Ashkenazi Jewish (ASJ)

AF:

0.170

AC:

756

AN:

4444

East Asian (EAS)

AF:

0.173

AC:

1272

AN:

7370

South Asian (SAS)

AF:

0.184

AC:

7855

AN:

42784

European-Finnish (FIN)

AF:

0.188

AC:

4476

AN:

23776

Middle Eastern (MID)

AF:

0.240

AC:

155

AN:

646

European-Non Finnish (NFE)

AF:

0.229

AC:

24716

AN:

107720

Other (OTH)

AF:

0.217

AC:

2033

AN:

9366

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

1587

3175

4762

6350

7937

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

200

400

600

800

1000

<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:

0.255

AC:

38757

AN:

152164

Hom.:

5181

Cov.:

AF XY:

0.253

AC XY:

18823

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.341

AC:

14173

AN:

41510

American (AMR)

AF:

0.258

AC:

3939

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.181

AC:

628

AN:

3472

East Asian (EAS)

AF:

0.169

AC:

875

AN:

5178

South Asian (SAS)

AF:

0.177

AC:

855

AN:

4832

European-Finnish (FIN)

AF:

0.187

AC:

1977

AN:

10592

Middle Eastern (MID)

AF:

0.253

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.229

AC:

15595

AN:

67980

Other (OTH)

AF:

0.245

AC:

517

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1501

3002

4504

6005

7506

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<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:

0.242

Hom.:

554

Bravo

AF:

0.263

Asia WGS

AF:

0.139

AC:

484

AN:

3476

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.111

AC:

13600

AN:

122600

Turkish Variome

AF:

0.206

AC:

318

AN:

1546

Hom.:

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.183

AC:

1638

AN:

8960

Hom.:

154

ABraOM SABE-WGS-1171

AF:

0.266

AC:

622

AN:

2342

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

9.3

(source)

DANN

Benign

0.75

PhyloP100

-0.81

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

Local populations

ClinVar

Computational scores

Splicing

Publications

Other links and lift over