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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_039682.1(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
NR_039682.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.984

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
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

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

GnomAD3 exomes

AF:

0.0939

AC:

AN:

362

Hom.:

AF XY:

0.0941

AC XY:

AN XY:

202

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

Gnomad4 AFR exome

AF:

0.419

Gnomad4 AMR exome

AF:

0.375

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0909

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.106

Gnomad4 OTH exome

AF:

0.193

GnomAD4 genome

AF:

0.219

AC:

33271

AN:

151956

Hom.:

5515

Cov.:

AF XY:

0.219

AC XY:

16248

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.459

Gnomad4 AMR

AF:

0.239

Gnomad4 ASJ

AF:

0.107

Gnomad4 EAS

AF:

0.168

Gnomad4 SAS

AF:

0.143

Gnomad4 FIN

AF:

0.119

Gnomad4 NFE

AF:

0.102

Gnomad4 OTH

AF:

0.170

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

DANN

Benign

0.74

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over