rs56075814

Variant names:

• chr1-207802604-T-C
• rs56075814
• ENST00000710905.2:n.639A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000710905.2(MIR29B2CHG):​n.639A>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 0.2 in 469,686 control chromosomes in the GnomAD database, including 10,319 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 0.19 (3079 hom., cov: 32)
  • Exomes 𝑓: 0.20 (7240 hom.)
• Consequence: MIR29B2CHG ENST00000710905.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428
• Publications: 16 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR29B2CHG	NR_135298.1	n.980A>G		non_coding_transcript_exon_variant	Exon 5 of 5
MIR29B2CHG	NR_135299.1	n.1165A>G		non_coding_transcript_exon_variant	Exon 6 of 6
MIR29B2	NR_029518.1	n.-81A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR29B2CHG	ENST00000710905.2	n.639A>G		non_coding_transcript_exon_variant	Exon 5 of 5
MIR29B2CHG	ENST00000710901.1	n.662+3401A>G		intron_variant	Intron 5 of 5
MIR29B2CHG	ENST00000710902.1	n.569+13325A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29646 AN: 151980 Hom.: 3072 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.00617

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.171

GnomAD4 exome AF: 0.202 AC: 64090 AN: 317588 Hom.: 7240 Cov.: 0 AF XY: 0.196 AC XY: 35043 AN XY: 178514

African (AFR) AF: 0.174 AC: 1542 AN: 8862

American (AMR) AF: 0.301 AC: 8984 AN: 29858

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 1152 AN: 8842

East Asian (EAS) AF: 0.00599 AC: 73 AN: 12188

South Asian (SAS) AF: 0.163 AC: 9396 AN: 57718

European-Finnish (FIN) AF: 0.217 AC: 6462 AN: 29794

Middle Eastern (MID) AF: 0.123 AC: 318 AN: 2586

European-Non Finnish (NFE) AF: 0.218 AC: 33554 AN: 153810

Other (OTH) AF: 0.187 AC: 2609 AN: 13930

GnomAD4 genome AF: 0.195 AC: 29655 AN: 152098 Hom.: 3079 Cov.: 32 AF XY: 0.193 AC XY: 14382 AN XY: 74362

African (AFR) AF: 0.176 AC: 7307 AN: 41486

American (AMR) AF: 0.242 AC: 3694 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3472

East Asian (EAS) AF: 0.00599 AC: 31 AN: 5174

South Asian (SAS) AF: 0.142 AC: 688 AN: 4830

European-Finnish (FIN) AF: 0.221 AC: 2327 AN: 10534

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14617 AN: 67996

Other (OTH) AF: 0.169 AC: 357 AN: 2110

Alfa AF: 0.202 Hom.: 378

Bravo AF: 0.197

Asia WGS AF: 0.0790 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.0
DANN	Benign	0.81
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs56075814; hg19: chr1-207975949; COSMIC: COSV66080695;