Genetic Variant MIR4472-1:n.61G>C (chr8-142176399-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000584349.1(MIR4472-1):n.61G>C 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 0.217 in 154,140 control chromosomes in the GnomAD database, including 5,534 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 0.22 ( 5515 hom., cov: 32)

Exomes 𝑓: 0.094 ( 19 hom. )

Consequence

MIR4472-1
ENST00000584349.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.984

Publications

12 publications found

Variant links:

Genes affected

MIR4472-1 (HGNC:41644): (microRNA 4472-1) 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]

MIR4472-1 links:

ENSG00000287332 (HGNC:):

ENSG00000287332 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4472-1	NR_039682.1 link	n.61G>C		non_coding_transcript_exon_variant	Exon 1 of 1
MIR4472-1	unassigned_transcript_1547	n.4G>C		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR4472-1	ENST00000584349.1 link	n.61G>C	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000287332	ENST00000662748.1 link	n.366+8763C>G	intron_variant	Intron 1 of 1
ENSG00000287332	ENST00000748267.1 link	n.669+8763C>G	intron_variant	Intron 2 of 5
ENSG00000287332	ENST00000748268.1 link	n.712+8763C>G	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33211

AN:

151838

Hom.:

5502

Cov.:

show subpopulations

Gnomad AFR

AF:

0.459

Gnomad AMI

AF:

0.0956

Gnomad AMR

AF:

0.239

Gnomad ASJ

AF:

0.107

Gnomad EAS

AF:

0.168

Gnomad SAS

AF:

0.144

Gnomad FIN

AF:

0.119

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.171

GnomAD2 exomes

AF:

0.0939

AC:

AN:

362

AF XY:

0.0941

show subpopulations

Gnomad AFR exome

AF:

0.500

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0954

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0939

AC:

205

AN:

2184

Hom.:

Cov.:

AF XY:

0.106

AC XY:

116

AN XY:

1092

show subpopulations

African (AFR)

AF:

0.419

AC:

AN:

American (AMR)

AF:

0.375

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.0909

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.0651

AC:

106

AN:

1628

European-Non Finnish (NFE)

AF:

0.106

AC:

AN:

188

Other (OTH)

AF:

0.193

AC:

AN:

192

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.219

AC:

33271

AN:

151956

Hom.:

5515

Cov.:

AF XY:

0.219

AC XY:

16248

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.459

AC:

18989

AN:

41392

American (AMR)

AF:

0.239

AC:

3655

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.107

AC:

371

AN:

3468

East Asian (EAS)

AF:

0.168

AC:

870

AN:

5164

South Asian (SAS)

AF:

0.143

AC:

683

AN:

4788

European-Finnish (FIN)

AF:

0.119

AC:

1265

AN:

10598

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.102

AC:

6959

AN:

67952

Other (OTH)

AF:

0.170

AC:

359

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1123

2247

3370

4494

5617

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

316

632

948

1264

1580

<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:

0.0849

Hom.:

150

Bravo

AF:

0.236

Asia WGS

AF:

0.177

AC:

614

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.7

(source)

DANN

Benign

0.74

PhyloP100

0.98

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