rs6542147

Positions:

• chr2-113583086-G-A

Variant summary

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

The NR_031632.1(MIR1302-3):​n.11C>T 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 0.49 (0 hom., cov: 64)
  • Exomes 𝑓: 0.49 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR1302-3 NR_031632.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

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]

(HGNC:):

ACMG classification

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	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR1302-3	NR_031632.1	n.11C>T		non_coding_transcript_exon_variant	1/1
LOC124907875	XR_007087204.1	n.945C>T		non_coding_transcript_exon_variant	1/3
LOC124907875	XR_007087203.1	n.961C>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR1302-3	ENST00000408128.1	n.11C>T		non_coding_transcript_exon_variant	1/1
	ENST00000666960.1	n.67C>T		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 72937 AN: 148014 Hom.: 0 Cov.: 64 FAILED QC

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.492

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.489 AC: 172254 AN: 352164 Hom.: 0 Cov.: 0 AF XY: 0.489 AC XY: 97685 AN XY: 199958

Gnomad4 AFR exome AF: 0.498

Gnomad4 AMR exome AF: 0.493

Gnomad4 ASJ exome AF: 0.487

Gnomad4 EAS exome AF: 0.498

Gnomad4 SAS exome AF: 0.487

Gnomad4 FIN exome AF: 0.494

Gnomad4 NFE exome AF: 0.487

Gnomad4 OTH exome AF: 0.489

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.493 AC: 72997 AN: 148136 Hom.: 0 Cov.: 64 AF XY: 0.493 AC XY: 35684 AN XY: 72384

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.492

Alfa AF: 0.482 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.6
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6542147; hg19: chr2-114340663;