Genetic Variant MIR4272:n.*108G>T (chr3-67225635-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000635924.1(MIR4272):n.*108G>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 153,476 control chromosomes in the GnomAD database, including 69,502 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 0.95 ( 68957 hom., cov: 33)

Exomes 𝑓: 0.97 ( 545 hom. )

Consequence

MIR4272
ENST00000635924.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.670

Publications

2 publications found

Variant links:

Genes affected

MIR4272 (HGNC:38303): (microRNA 4272) 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]

MIR4272 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=-0.98).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4272	NR_036234.1 link	n.*108G>T		downstream_gene_variant
MIR4272	unassigned_transcript_639	n.*118G>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4272	ENST00000635924.1 link	n.*108G>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.951

AC:

144674

AN:

152200

Hom.:

68896

Cov.:

show subpopulations

Gnomad AFR

AF:

0.899

Gnomad AMI

AF:

0.979

Gnomad AMR

AF:

0.926

Gnomad ASJ

AF:

0.928

Gnomad EAS

AF:

0.959

Gnomad SAS

AF:

0.987

Gnomad FIN

AF:

0.993

Gnomad MID

AF:

0.943

Gnomad NFE

AF:

0.979

Gnomad OTH

AF:

0.945

GnomAD4 exome

AF:

0.971

AC:

1123

AN:

1156

Hom.:

545

AF XY:

0.974

AC XY:

641

AN XY:

658

show subpopulations

African (AFR)

AF:

0.844

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.991

AC:

424

AN:

428

Middle Eastern (MID)

AF:

0.964

AC:

397

AN:

412

European-Non Finnish (NFE)

AF:

0.973

AC:

177

AN:

182

Other (OTH)

AF:

0.933

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

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:

0.951

AC:

144795

AN:

152320

Hom.:

68957

Cov.:

AF XY:

0.953

AC XY:

70948

AN XY:

74470

show subpopulations

African (AFR)

AF:

0.899

AC:

37348

AN:

41550

American (AMR)

AF:

0.926

AC:

14169

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.928

AC:

3221

AN:

3472

East Asian (EAS)

AF:

0.959

AC:

4964

AN:

5178

South Asian (SAS)

AF:

0.987

AC:

4763

AN:

4826

European-Finnish (FIN)

AF:

0.993

AC:

10556

AN:

10628

Middle Eastern (MID)

AF:

0.942

AC:

277

AN:

294

European-Non Finnish (NFE)

AF:

0.979

AC:

66603

AN:

68040

Other (OTH)

AF:

0.946

AC:

2001

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

366

732

1099

1465

1831

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

912

1824

2736

3648

4560

<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:

0.953

Hom.:

12031

Bravo

AF:

0.940

Asia WGS

AF:

0.980

AC:

3408

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.51

(source)

DANN

Benign

0.44

PhyloP100

-0.67

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