Variant rs12803915 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_030343.1(MIR612):n.51G>A 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 0.17 in 490,522 control chromosomes in the GnomAD database, including 7,664 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 0.17 ( 2285 hom., cov: 30)

Exomes 𝑓: 0.17 ( 5379 hom. )

Consequence

MIR612
NR_030343.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.44

Variant links:

Genes affected

MIR612 (HGNC:32868): (microRNA 612) 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]

MIR612 links:

NEAT1 (HGNC:30815): (nuclear paraspeckle assembly transcript 1) This gene produces a long non-coding RNA (lncRNA) transcribed from the multiple endocrine neoplasia locus. This lncRNA is retained in the nucleus where it forms the core structural component of the paraspeckle sub-organelles. It may act as a transcriptional regulator for numerous genes, including some genes involved in cancer progression. [provided by RefSeq, Mar 2015]

NEAT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR612	NR_030343.1 linkuse as main transcript	n.51G>A		non_coding_transcript_exon_variant	1/1
NEAT1	NR_131012.1 linkuse as main transcript	n.21711G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR612	ENST00000384994.1 linkuse as main transcript	n.51G>A		non_coding_transcript_exon_variant	1/1
NEAT1	ENST00000501122.2 linkuse as main transcript	n.21711G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25323

AN:

151834

Hom.:

2283

Cov.:

show subpopulations

Gnomad AFR

AF:

0.123

Gnomad AMI

AF:

0.334

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.193

Gnomad EAS

AF:

0.146

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.194

Gnomad NFE

AF:

0.209

Gnomad OTH

AF:

0.159

GnomAD3 exomes

AF:

0.164

AC:

29712

AN:

180892

Hom.:

2663

AF XY:

0.164

AC XY:

15893

AN XY:

96738

show subpopulations

Gnomad AFR exome

AF:

0.116

Gnomad AMR exome

AF:

0.130

Gnomad ASJ exome

AF:

0.193

Gnomad EAS exome

AF:

0.146

Gnomad SAS exome

AF:

0.118

Gnomad FIN exome

AF:

0.121

Gnomad NFE exome

AF:

0.207

Gnomad OTH exome

AF:

0.178

GnomAD4 exome

AF:

0.172

AC:

58085

AN:

338566

Hom.:

5379

Cov.:

AF XY:

0.169

AC XY:

32339

AN XY:

191724

show subpopulations

Gnomad4 AFR exome

AF:

0.125

Gnomad4 AMR exome

AF:

0.131

Gnomad4 ASJ exome

AF:

0.193

Gnomad4 EAS exome

AF:

0.142

Gnomad4 SAS exome

AF:

0.118

Gnomad4 FIN exome

AF:

0.124

Gnomad4 NFE exome

AF:

0.208

Gnomad4 OTH exome

AF:

0.181

GnomAD4 genome

AF:

0.167

AC:

25341

AN:

151956

Hom.:

2285

Cov.:

AF XY:

0.159

AC XY:

11838

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.123

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.193

Gnomad4 EAS

AF:

0.147

Gnomad4 SAS

AF:

0.109

Gnomad4 FIN

AF:

0.118

Gnomad4 NFE

AF:

0.209

Gnomad4 OTH

AF:

0.156

Alfa

AF:

0.193

Hom.:

1493

Bravo

AF:

0.170

Asia WGS

AF:

0.113

AC:

396

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

Cadd

Benign

7.7

Dann

Benign

0.79

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.3

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