1-207802560-C-T

Variant names:

• chr1-207802560-C-T
• rs78876157
• ENST00000710905.2:n.683G>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984
• Publications: 6 publications found

Genes affected

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

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]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS2: High Homozygotes in GnomAdExome4 at 17 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_135298.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR29B2CHG	NR_135298.1		n.1024G>A		non_coding_transcript_exon	Exon 5 of 5
	MIR29B2CHG	NR_135299.1		n.1209G>A		non_coding_transcript_exon	Exon 6 of 6
	MIR29B2	NR_029518.1		n.-37G>A		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR29B2CHG	ENST00000710905.2		n.683G>A		non_coding_transcript_exon	Exon 5 of 5
	MIR29B2CHG	ENST00000710901.1		n.662+3445G>A		intron	N/A
	MIR29B2CHG	ENST00000710902.1		n.569+13369G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00583 AC: 886 AN: 152092 Hom.: 1 Cov.: 32

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

GnomAD2 exomes AF: 0.00575 AC: 1412 AN: 245726 AF XY: 0.00596

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 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.: 17 Cov.: 0 AF XY: 0.00584 AC XY: 1246 AN XY: 213502

African (AFR) AF: 0.00216 AC: 22 AN: 10170

American (AMR) AF: 0.00678 AC: 240 AN: 35390

Ashkenazi Jewish (ASJ) AF: 0.00427 AC: 49 AN: 11472

East Asian (EAS) AF: 0.0000769 AC: 1 AN: 12998

South Asian (SAS) AF: 0.00106 AC: 70 AN: 65770

European-Finnish (FIN) AF: 0.000747 AC: 24 AN: 32142

Middle Eastern (MID) AF: 0.00393 AC: 11 AN: 2802

European-Non Finnish (NFE) AF: 0.00921 AC: 1728 AN: 187624

Other (OTH) AF: 0.00579 AC: 95 AN: 16402

GnomAD4 genome AF: 0.00583 AC: 887 AN: 152210 Hom.: 1 Cov.: 32 AF XY: 0.00564 AC XY: 420 AN XY: 74420

African (AFR) AF: 0.00229 AC: 95 AN: 41498

American (AMR) AF: 0.00818 AC: 125 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00404 AC: 14 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4822

European-Finnish (FIN) AF: 0.000754 AC: 8 AN: 10606

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00914 AC: 622 AN: 68036

Other (OTH) AF: 0.00803 AC: 17 AN: 2116

Alfa AF: 0.00837 Hom.: 8

Bravo AF: 0.00653

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.64
PhyloP100		-0.98

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs78876157; hg19: chr1-207975905;