Variant 14-101065517-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NR_030155.1(MIR412):n.71A>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 0.367 in 534,354 control chromosomes in the GnomAD database, including 42,800 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 0.34 ( 11231 hom., cov: 32)

Exomes 𝑓: 0.38 ( 31569 hom. )

Consequence

MIR412
NR_030155.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.33

Variant links:

Genes affected

MIR412 (HGNC:32064): (microRNA 412) 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]

MIR412 links:

MEG9 (HGNC:43874): (maternally expressed 9)

MEG9 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.33).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR412	NR_030155.1 linkuse as main transcript	n.71A>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons
MIR412	ENST00000362142.2 linkuse as main transcript	n.71A>G	mature_miRNA_variant	1/1
MEG9	ENST00000699461.1 linkuse as main transcript	n.496+3910A>G	intron_variant, non_coding_transcript_variant
MEG9	ENST00000699462.1 linkuse as main transcript	n.219+1150A>G	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

51238

AN:

152012

Hom.:

11241

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0974

Gnomad AMI

AF:

0.599

Gnomad AMR

AF:

0.306

Gnomad ASJ

AF:

0.448

Gnomad EAS

AF:

0.0364

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.522

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.483

Gnomad OTH

AF:

0.358

GnomAD3 exomes

AF:

0.353

AC:

88479

AN:

250972

Hom.:

19035

AF XY:

0.360

AC XY:

48905

AN XY:

135872

show subpopulations

Gnomad AFR exome

AF:

0.0928

Gnomad AMR exome

AF:

0.212

Gnomad ASJ exome

AF:

0.436

Gnomad EAS exome

AF:

0.0362

Gnomad SAS exome

AF:

0.224

Gnomad FIN exome

AF:

0.518

Gnomad NFE exome

AF:

0.477

Gnomad OTH exome

AF:

0.401

GnomAD4 exome

AF:

0.380

AC:

145135

AN:

382224

Hom.:

31569

Cov.:

AF XY:

0.374

AC XY:

81282

AN XY:

217552

show subpopulations

Gnomad4 AFR exome

AF:

0.0924

Gnomad4 AMR exome

AF:

0.212

Gnomad4 ASJ exome

AF:

0.438

Gnomad4 EAS exome

AF:

0.0353

Gnomad4 SAS exome

AF:

0.231

Gnomad4 FIN exome

AF:

0.513

Gnomad4 NFE exome

AF:

0.475

Gnomad4 OTH exome

AF:

0.399

GnomAD4 genome

AF:

0.337

AC:

51227

AN:

152130

Hom.:

11231

Cov.:

AF XY:

0.335

AC XY:

24883

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.0972

Gnomad4 AMR

AF:

0.306

Gnomad4 ASJ

AF:

0.448

Gnomad4 EAS

AF:

0.0365

Gnomad4 SAS

AF:

0.215

Gnomad4 FIN

AF:

0.522

Gnomad4 NFE

AF:

0.483

Gnomad4 OTH

AF:

0.354

Alfa

AF:

0.418

Hom.:

7552

Bravo

AF:

0.313

Asia WGS

AF:

0.133

AC:

464

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

DANN

Benign

0.70

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