dbSNP rs58834075: MIR656:n.33C>G (chr14-101066756-C-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000385224.1(MIR656):n.33C>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 0.00000261 in 382,436 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)

Exomes 𝑓: 0.0000026 ( 0 hom. )

Consequence

MIR656
ENST00000385224.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.512

Publications

23 publications found

Variant links:

Genes affected

MIR656 (HGNC:32912): (microRNA 656) 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]

MIR656 links:

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

MEG9 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.23).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR656	NR_030392.1 link	n.33C>G	non_coding_transcript_exon_variant	Exon 1 of 1
MIR656	unassigned_transcript_2453	n.-10C>G	upstream_gene_variant
MIR656	unassigned_transcript_2452	n.*5C>G	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR656	ENST00000385224.1 link	n.33C>G	non_coding_transcript_exon_variant	Exon 1 of 1	6
MEG9	ENST00000699461.1 link	n.497-3686C>G	intron_variant	Intron 4 of 6
MEG9	ENST00000699462.1 link	n.219+2389C>G	intron_variant	Intron 1 of 3
MEG9	ENST00000818609.1 link	n.258+2389C>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000398

AC:

AN:

251018

AF XY:

0.00000736

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000882

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000261

AC:

AN:

382436

Hom.:

Cov.:

AF XY:

0.00000459

AC XY:

AN XY:

217720

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

10512

American (AMR)

AF:

0.00

AC:

AN:

36296

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11742

East Asian (EAS)

AF:

0.00

AC:

AN:

13176

South Asian (SAS)

AF:

0.00

AC:

AN:

66762

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32312

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2844

European-Non Finnish (NFE)

AF:

0.00000521

AC:

AN:

192064

Other (OTH)

AF:

0.00

AC:

AN:

16728

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

355

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.23

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

0.51

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over