Genetic Variant MIR29B2CHG:n.196G>A (chr1-207802560-C-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NR_135298.1(MIR29B2CHG):n.1024G>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 0.00593 in 526,980 control chromosomes in the GnomAD database, including 18 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 0.0058 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0060 ( 17 hom. )

Consequence

MIR29B2CHG
NR_135298.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.984

Variant links:

Genes affected

MIR29B2CHG (HGNC:32018): (MIR29B2 and MIR29C host gene)

MIR29B2CHG links:

MIR29B2 (HGNC:31620): (microRNA 29b-2) 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]

MIR29B2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BS2

High Homozygotes in GnomAdExome4 at 17 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR29B2CHG	NR_135298.1 link	n.1024G>A	non_coding_transcript_exon_variant	Exon 5 of 5
MIR29B2CHG	NR_135299.1 link	n.1209G>A	non_coding_transcript_exon_variant	Exon 6 of 6
MIR29B2	NR_029518.1 link	n.-37G>A	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
MIR29B2CHG	ENST00000710905.1 link	n.196G>A	non_coding_transcript_exon_variant	Exon 2 of 2
MIR29B2CHG	ENST00000710901.1 link	n.662+3445G>A	intron_variant	Intron 5 of 5
MIR29B2CHG	ENST00000710902.1 link	n.569+13369G>A	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.00583

AC:

886

AN:

152092

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00230

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00819

Gnomad ASJ

AF:

0.00404

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.000754

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00914

Gnomad OTH

AF:

0.00812

GnomAD3 exomes

AF:

0.00575

AC:

1412

AN:

245726

Hom.:

AF XY:

0.00596

AC XY:

793

AN XY:

133124

show subpopulations

Gnomad AFR exome

AF:

0.00188

Gnomad AMR exome

AF:

0.00646

Gnomad ASJ exome

AF:

0.00401

Gnomad EAS exome

AF:

0.0000553

Gnomad SAS exome

AF:

0.000977

Gnomad FIN exome

AF:

0.000605

Gnomad NFE exome

AF:

0.00939

Gnomad OTH exome

AF:

0.00621

GnomAD4 exome

AF:

0.00598

AC:

2240

AN:

374770

Hom.:

Cov.:

AF XY:

0.00584

AC XY:

1246

AN XY:

213502

show subpopulations

Gnomad4 AFR exome

AF:

0.00216

Gnomad4 AMR exome

AF:

0.00678

Gnomad4 ASJ exome

AF:

0.00427

Gnomad4 EAS exome

AF:

0.0000769

Gnomad4 SAS exome

AF:

0.00106

Gnomad4 FIN exome

AF:

0.000747

Gnomad4 NFE exome

AF:

0.00921

Gnomad4 OTH exome

AF:

0.00579

GnomAD4 genome

AF:

0.00583

AC:

887

AN:

152210

Hom.:

Cov.:

AF XY:

0.00564

AC XY:

420

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.00229

Gnomad4 AMR

AF:

0.00818

Gnomad4 ASJ

AF:

0.00404

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.000754

Gnomad4 NFE

AF:

0.00914

Gnomad4 OTH

AF:

0.00803

Alfa

AF:

0.00784

Hom.:

Bravo

AF:

0.00653

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.7

DANN

Benign

0.64

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