dbSNP rs2910164: MIR3142HG:n.286C>G (chr5-160485411-C-G) – ACMG Classification: Benign (-10 pts)

Variant summary

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

The ENST00000517927.1(MIR3142HG):n.286C>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 0.727 in 528,390 control chromosomes in the GnomAD database, including 141,782 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 0.70 ( 38097 hom., cov: 31)

Exomes 𝑓: 0.74 ( 103685 hom. )

Consequence

MIR3142HG
ENST00000517927.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.57

Variant links:

Genes affected

MIR3142HG (HGNC:51944): (MIR3142 host gene)

MIR3142HG links:

MIR146A (HGNC:31533): (microRNA 146a) 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. Some of the targets of the encoded miRNA are the transcripts for tumor necrosis factor, interleukin 1 receptor-associated kinase 1, interleukin 1-beta, TNF receptor-associated factor 6, and complement factor H. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2015]

MIR146A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR146A	NR_029701.1 link	n.60C>G	non_coding_transcript_exon_variant	Exon 1 of 1
MIR3142HG	NR_132748.1 link	n.303C>G	non_coding_transcript_exon_variant	Exon 2 of 2
MIR146A	unassigned_transcript_889	n.4C>G	non_coding_transcript_exon_variant	Exon 1 of 1
MIR146A	unassigned_transcript_888	n.*18C>G	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR3142HG	ENST00000517927.1 link	n.286C>G	non_coding_transcript_exon_variant	Exon 2 of 2	1
MIR146A	ENST00000385201.1 link	n.60C>G	non_coding_transcript_exon_variant	Exon 1 of 1	6
MIR3142HG	ENST00000642173.1 link	n.189C>G	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.702

AC:

106630

AN:

151942

Hom.:

38071

Cov.:

show subpopulations

Gnomad AFR

AF:

0.607

Gnomad AMI

AF:

0.682

Gnomad AMR

AF:

0.708

Gnomad ASJ

AF:

0.783

Gnomad EAS

AF:

0.380

Gnomad SAS

AF:

0.705

Gnomad FIN

AF:

0.787

Gnomad MID

AF:

0.655

Gnomad NFE

AF:

0.766

Gnomad OTH

AF:

0.687

GnomAD3 exomes

AF:

0.713

AC:

175623

AN:

246292

Hom.:

64108

AF XY:

0.719

AC XY:

95733

AN XY:

133108

show subpopulations

Gnomad AFR exome

AF:

0.598

Gnomad AMR exome

AF:

0.694

Gnomad ASJ exome

AF:

0.777

Gnomad EAS exome

AF:

0.372

Gnomad SAS exome

AF:

0.720

Gnomad FIN exome

AF:

0.784

Gnomad NFE exome

AF:

0.770

Gnomad OTH exome

AF:

0.730

GnomAD4 exome

AF:

0.737

AC:

277348

AN:

376330

Hom.:

103685

Cov.:

AF XY:

0.738

AC XY:

157630

AN XY:

213566

show subpopulations

Gnomad4 AFR exome

AF:

0.599

Gnomad4 AMR exome

AF:

0.694

Gnomad4 ASJ exome

AF:

0.777

Gnomad4 EAS exome

AF:

0.376

Gnomad4 SAS exome

AF:

0.727

Gnomad4 FIN exome

AF:

0.782

Gnomad4 NFE exome

AF:

0.772

Gnomad4 OTH exome

AF:

0.733

GnomAD4 genome

AF:

0.702

AC:

106701

AN:

152060

Hom.:

38097

Cov.:

AF XY:

0.702

AC XY:

52221

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.607

Gnomad4 AMR

AF:

0.709

Gnomad4 ASJ

AF:

0.783

Gnomad4 EAS

AF:

0.380

Gnomad4 SAS

AF:

0.705

Gnomad4 FIN

AF:

0.787

Gnomad4 NFE

AF:

0.766

Gnomad4 OTH

AF:

0.688

Alfa

AF:

0.755

Hom.:

14093

Bravo

AF:

0.691

Asia WGS

AF:

0.549

AC:

1913

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

DANN

Benign

0.76

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