Genetic Variant ENST00000408128.1:n.46G>A (chr2-113583051-C-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000408128.1(MIR1302-3):n.46G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.29 ( 0 hom., cov: 70)

Exomes 𝑓: 0.15 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MIR1302-3
ENST00000408128.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.936

Variant links:

Genes affected

MIR1302-3 (HGNC:35295): (microRNA 1302-3) 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]

MIR1302-3 links:

ENSG00000287165 (HGNC:):

ENSG00000287165 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR1302-3	NR_031632.1 link	n.46G>A	non_coding_transcript_exon_variant	Exon 1 of 1
LOC124907875	XR_007087203.1 link	n.996G>A	non_coding_transcript_exon_variant	Exon 1 of 2
LOC124907875	XR_007087204.1 link	n.980G>A	non_coding_transcript_exon_variant	Exon 1 of 3
MIR1302-3	unassigned_transcript_479	n.-27G>A	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR1302-3	ENST00000408128.1 link	n.46G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000287165	ENST00000666960.1 link	n.102G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

29328

AN:

102706

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.381

Gnomad AMI

AF:

0.338

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.283

Gnomad EAS

AF:

0.337

Gnomad SAS

AF:

0.275

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.241

Gnomad OTH

AF:

0.283

GnomAD3 exomes

AF:

0.0408

AC:

6560

AN:

160910

Hom.:

AF XY:

0.0402

AC XY:

3533

AN XY:

87976

show subpopulations

Gnomad AFR exome

AF:

0.0870

Gnomad AMR exome

AF:

0.0339

Gnomad ASJ exome

AF:

0.0710

Gnomad EAS exome

AF:

0.0661

Gnomad SAS exome

AF:

0.0635

Gnomad FIN exome

AF:

0.0307

Gnomad NFE exome

AF:

0.0278

Gnomad OTH exome

AF:

0.0457

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.146

AC:

29225

AN:

200520

Hom.:

Cov.:

AF XY:

0.149

AC XY:

17092

AN XY:

114662

show subpopulations

Gnomad4 AFR exome

AF:

0.260

Gnomad4 AMR exome

AF:

0.109

Gnomad4 ASJ exome

AF:

0.171

Gnomad4 EAS exome

AF:

0.219

Gnomad4 SAS exome

AF:

0.187

Gnomad4 FIN exome

AF:

0.115

Gnomad4 NFE exome

AF:

0.131

Gnomad4 OTH exome

AF:

0.148

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.286

AC:

29361

AN:

102784

Hom.:

Cov.:

AF XY:

0.284

AC XY:

14224

AN XY:

50138

show subpopulations

Gnomad4 AFR

AF:

0.381

Gnomad4 AMR

AF:

0.263

Gnomad4 ASJ

AF:

0.283

Gnomad4 EAS

AF:

0.337

Gnomad4 SAS

AF:

0.275

Gnomad4 FIN

AF:

0.209

Gnomad4 NFE

AF:

0.241

Gnomad4 OTH

AF:

0.279

Alfa

AF:

0.182

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.1

DANN

Benign

0.73

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