dbSNP rs17759989: MIR633:n.36A>G (chr17-62944250-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NR_030363.1(MIR633):n.36A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0283 in 533,120 control chromosomes in the GnomAD database, including 303 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 0.028 ( 78 hom., cov: 32)

Exomes 𝑓: 0.028 ( 225 hom. )

Consequence

MIR633
NR_030363.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.464

Publications

12 publications found

Variant links:

Genes affected

MIR633 (HGNC:32889): (microRNA 633) 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]

MIR633 links:

ENSG00000283538 (HGNC:):

ENSG00000283538 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=-0.84).

BS1

Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0278 (4232/152286) while in subpopulation SAS AF = 0.0367 (177/4824). AF 95% confidence interval is 0.0323. There are 78 homozygotes in GnomAd4. There are 2069 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 78 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_030363.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR633	NR_030363.1		n.36A>G		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIR633	ENST00000384821.1	TSL:6	n.36A>G	non_coding_transcript_exon	Exon 1 of 1
ENSG00000283538	ENST00000636248.2	TSL:5	n.51-7385T>C	intron	N/A
ENSG00000283538	ENST00000650312.1		n.128-7385T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0277

AC:

4221

AN:

152168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0313

Gnomad AMI

AF:

0.0384

Gnomad AMR

AF:

0.0195

Gnomad ASJ

AF:

0.00864

Gnomad EAS

AF:

0.00557

Gnomad SAS

AF:

0.0360

Gnomad FIN

AF:

0.0382

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0278

Gnomad OTH

AF:

0.0263

GnomAD2 exomes

AF:

0.0258

AC:

6348

AN:

245632

AF XY:

0.0268

show subpopulations

Gnomad AFR exome

AF:

0.0325

Gnomad AMR exome

AF:

0.0113

Gnomad ASJ exome

AF:

0.0103

Gnomad EAS exome

AF:

0.00618

Gnomad FIN exome

AF:

0.0357

Gnomad NFE exome

AF:

0.0290

Gnomad OTH exome

AF:

0.0296

GnomAD4 exome

AF:

0.0284

AC:

10833

AN:

380834

Hom.:

225

Cov.:

AF XY:

0.0297

AC XY:

6437

AN XY:

216822

show subpopulations

African (AFR)

AF:

0.0333

AC:

347

AN:

10414

American (AMR)

AF:

0.0110

AC:

395

AN:

36006

Ashkenazi Jewish (ASJ)

AF:

0.0109

AC:

127

AN:

11688

East Asian (EAS)

AF:

0.00502

AC:

AN:

13156

South Asian (SAS)

AF:

0.0371

AC:

2463

AN:

66302

European-Finnish (FIN)

AF:

0.0351

AC:

1128

AN:

32174

Middle Eastern (MID)

AF:

0.0570

AC:

162

AN:

2842

European-Non Finnish (NFE)

AF:

0.0293

AC:

5616

AN:

191572

Other (OTH)

AF:

0.0317

AC:

529

AN:

16680

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

581

1163

1744

2326

2907

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

138

184

230

<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:

0.0278

AC:

4232

AN:

152286

Hom.:

Cov.:

AF XY:

0.0278

AC XY:

2069

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.0313

AC:

1302

AN:

41556

American (AMR)

AF:

0.0195

AC:

298

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00864

AC:

AN:

3472

East Asian (EAS)

AF:

0.00559

AC:

AN:

5190

South Asian (SAS)

AF:

0.0367

AC:

177

AN:

4824

European-Finnish (FIN)

AF:

0.0382

AC:

405

AN:

10608

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0278

AC:

1892

AN:

68026

Other (OTH)

AF:

0.0275

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

206

412

618

824

1030

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

162

216

270

<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:

0.0279

Hom.:

Bravo

AF:

0.0260

Asia WGS

AF:

0.0340

AC:

119

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.0

(source)

DANN

Benign

0.32

PhyloP100

0.46

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