7-129770387-C-T

Variant names:

• chr7-129770387-C-T
• rs76481776
• ENST00000385255.3:n.106G>A

Variant summary

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

The NR_029614.1(MIR182):​n.106G>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 0.0617 in 531,246 control chromosomes in the GnomAD database, including 1,257 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 0.058 (336 hom., cov: 33)
  • Exomes 𝑓: 0.063 (921 hom.)
• Consequence: MIR182 NR_029614.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 58 publications found

Genes affected

MIR182 (HGNC:31553): (microRNA 182) 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]

ENSG00000286380 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0854 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_029614.1. 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
	MIR182	NR_029614.1		n.106G>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR182	ENST00000385255.3	TSL:6	n.106G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000286380	ENST00000710872.1		n.432-6981G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0579 AC: 8801 AN: 152116 Hom.: 336 Cov.: 33

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.0537

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.0241

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0873

Gnomad OTH AF: 0.0593

GnomAD2 exomes AF: 0.0586 AC: 14621 AN: 249368 AF XY: 0.0592

Gnomad AFR exome AF: 0.0140

Gnomad AMR exome AF: 0.0363

Gnomad ASJ exome AF: 0.0154

Gnomad EAS exome AF: 0.0177

Gnomad FIN exome AF: 0.0808

Gnomad NFE exome AF: 0.0871

Gnomad OTH exome AF: 0.0694

GnomAD4 exome AF: 0.0632 AC: 23967 AN: 379012 Hom.: 921 Cov.: 0 AF XY: 0.0605 AC XY: 13044 AN XY: 215560

African (AFR) AF: 0.0170 AC: 178 AN: 10464

American (AMR) AF: 0.0371 AC: 1344 AN: 36202

Ashkenazi Jewish (ASJ) AF: 0.0168 AC: 196 AN: 11692

East Asian (EAS) AF: 0.0183 AC: 240 AN: 13080

South Asian (SAS) AF: 0.0222 AC: 1482 AN: 66620

European-Finnish (FIN) AF: 0.0801 AC: 2558 AN: 31936

Middle Eastern (MID) AF: 0.0771 AC: 199 AN: 2582

European-Non Finnish (NFE) AF: 0.0877 AC: 16656 AN: 189888

Other (OTH) AF: 0.0673 AC: 1114 AN: 16548

GnomAD4 genome AF: 0.0578 AC: 8795 AN: 152234 Hom.: 336 Cov.: 33 AF XY: 0.0572 AC XY: 4259 AN XY: 74440

African (AFR) AF: 0.0167 AC: 693 AN: 41540

American (AMR) AF: 0.0536 AC: 819 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3466

East Asian (EAS) AF: 0.0183 AC: 95 AN: 5190

South Asian (SAS) AF: 0.0239 AC: 115 AN: 4816

European-Finnish (FIN) AF: 0.0836 AC: 887 AN: 10614

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0873 AC: 5936 AN: 68010

Other (OTH) AF: 0.0587 AC: 124 AN: 2112

Alfa AF: 0.0602 Hom.: 157

Bravo AF: 0.0537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.5
DANN	Benign	0.83
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs76481776; hg19: chr7-129410227;