dbSNP rs72631832: MIR345:n.8C>T (chr14-100307866-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000362114.1(MIR345):n.8C>T 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 0.0182 in 449,978 control chromosomes in the GnomAD database, including 97 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 0.016 ( 27 hom., cov: 33)

Exomes 𝑓: 0.019 ( 70 hom. )

Consequence

MIR345
ENST00000362114.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.650

Publications

5 publications found

Variant links:

Genes affected

MIR345 (HGNC:31779): (microRNA 345) 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]

MIR345 links:

Genome browser will be placed here

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=-0.61).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0164 (2495/152322) while in subpopulation NFE AF = 0.0254 (1727/68016). AF 95% confidence interval is 0.0244. There are 27 homozygotes in GnomAd4. There are 1192 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 27 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR345	NR_029906.1 link	n.8C>T	non_coding_transcript_exon_variant	Exon 1 of 1
MIR345	unassigned_transcript_2355	n.-10C>T	upstream_gene_variant
MIR345	unassigned_transcript_2356	n.-46C>T	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR345	ENST00000362114.1 link	n.8C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.0164

AC:

2495

AN:

152204

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00386

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.0100

Gnomad ASJ

AF:

0.0144

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00993

Gnomad FIN

AF:

0.0292

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0254

Gnomad OTH

AF:

0.0115

GnomAD2 exomes

AF:

0.0166

AC:

2559

AN:

153974

AF XY:

0.0173

show subpopulations

Gnomad AFR exome

AF:

0.00429

Gnomad AMR exome

AF:

0.00760

Gnomad ASJ exome

AF:

0.0133

Gnomad EAS exome

AF:

0.000179

Gnomad FIN exome

AF:

0.0276

Gnomad NFE exome

AF:

0.0245

Gnomad OTH exome

AF:

0.0160

GnomAD4 exome

AF:

0.0191

AC:

5696

AN:

297656

Hom.:

Cov.:

AF XY:

0.0188

AC XY:

3191

AN XY:

169374

show subpopulations

African (AFR)

AF:

0.00449

AC:

AN:

8232

American (AMR)

AF:

0.00718

AC:

187

AN:

26030

Ashkenazi Jewish (ASJ)

AF:

0.0155

AC:

154

AN:

9956

East Asian (EAS)

AF:

0.00

AC:

AN:

9016

South Asian (SAS)

AF:

0.0119

AC:

689

AN:

57724

European-Finnish (FIN)

AF:

0.0283

AC:

781

AN:

27566

Middle Eastern (MID)

AF:

0.00784

AC:

AN:

2680

European-Non Finnish (NFE)

AF:

0.0250

AC:

3593

AN:

143502

Other (OTH)

AF:

0.0181

AC:

234

AN:

12950

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.527

Heterozygous variant carriers

248

495

743

990

1238

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.0164

AC:

2495

AN:

152322

Hom.:

Cov.:

AF XY:

0.0160

AC XY:

1192

AN XY:

74478

show subpopulations

African (AFR)

AF:

0.00385

AC:

160

AN:

41582

American (AMR)

AF:

0.0100

AC:

153

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0144

AC:

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5192

South Asian (SAS)

AF:

0.00994

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0292

AC:

310

AN:

10614

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0254

AC:

1727

AN:

68016

Other (OTH)

AF:

0.0114

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

124

248

371

495

619

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

150

<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:

0.0211

Hom.:

Bravo

AF:

0.0138

Asia WGS

AF:

0.00693

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

9.0

(source)

DANN

Benign

0.70

PhyloP100

-0.65

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over