Genetic Variant ENST00000385255.3:n.94G>A (chr7-129770399-C-T) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The ENST00000385255.3(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
ENST00000385255.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.25

Variant links:

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]

MIR182 links:

ENSG00000286380 (HGNC:):

ENSG00000286380 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=-0.79).

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR182	NR_029614.1 link	n.94G>A	non_coding_transcript_exon_variant	Exon 1 of 1
MIR182	unassigned_transcript_1304	n.*7G>A	downstream_gene_variant
MIR182	unassigned_transcript_1305	n.*48G>A	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR182	ENST00000385255.3 link	n.94G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000286380	ENST00000710872.1 link	n.432-6993G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.00306

AC:

465

AN:

152182

Hom.:

Cov.:

show subpopulations

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.:

AF XY:

0.00373

AC XY:

505

AN XY:

135544

show subpopulations

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.:

Cov.:

AF XY:

0.00402

AC XY:

871

AN XY:

216616

show subpopulations

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.:

Cov.:

AF XY:

0.00313

AC XY:

233

AN XY:

74466

show subpopulations

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.:

Bravo

AF:

0.00305

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

-0.79

CADD

Benign

DANN

Benign

0.90

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