7-129770399-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NR_029614.1(MIR182):n.94G>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 0.0036 in 532,912 control chromosomes in the GnomAD database, including 11 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 0.0030 (2 hom., cov: 32)
  • Exomes 𝑓: 0.0038 (9 hom.)
• Consequence: MIR182 NR_029614.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BS2: High Homozygotes in GnomAd at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR182	NR_029614.1	n.94G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR182	ENST00000385255.3	n.94G>A		non_coding_transcript_exon_variant	1/1
	ENST00000710872.1	n.432-6993G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00306 AC: 465 AN: 152182 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.00106

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00334

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00497

Gnomad FIN AF: 0.00122

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00460

Gnomad OTH AF: 0.00478

GnomAD3 exomes AF: 0.00345 AC: 864 AN: 250078 Hom.: 4 AF XY: 0.00373 AC XY: 505 AN XY: 135544

Gnomad AFR exome AF: 0.000807

Gnomad AMR exome AF: 0.00104

Gnomad ASJ exome AF: 0.00230

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00537

Gnomad FIN exome AF: 0.00102

Gnomad NFE exome AF: 0.00521

Gnomad OTH exome AF: 0.00294

GnomAD4 exome AF: 0.00383 AC: 1457 AN: 380612 Hom.: 9 Cov.: 0 AF XY: 0.00402 AC XY: 871 AN XY: 216616

Gnomad4 AFR exome AF: 0.000953

Gnomad4 AMR exome AF: 0.000966

Gnomad4 ASJ exome AF: 0.00222

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00543

Gnomad4 FIN exome AF: 0.00119

Gnomad4 NFE exome AF: 0.00486

Gnomad4 OTH exome AF: 0.00343

GnomAD4 genome AF: 0.00305 AC: 464 AN: 152300 Hom.: 2 Cov.: 32 AF XY: 0.00313 AC XY: 233 AN XY: 74466

Gnomad4 AFR AF: 0.00106

Gnomad4 AMR AF: 0.00333

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00498

Gnomad4 FIN AF: 0.00122

Gnomad4 NFE AF: 0.00459

Gnomad4 OTH AF: 0.00473

Alfa AF: 0.00398 Hom.: 2

Bravo AF: 0.00305

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	14
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs80041074; hg19: chr7-129410239;