rs6542147

Variant names:

• chr2-113583086-G-A
• rs6542147
• ENST00000408128.1:n.11C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000408128.1(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 ENST00000408128.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 5 publications found

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]

ENSG00000287165 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR1302-3	NR_031632.1	n.11C>T		non_coding_transcript_exon_variant	Exon 1 of 1
LOC124907875	XR_007087203.1	n.961C>T		non_coding_transcript_exon_variant	Exon 1 of 2
LOC124907875	XR_007087204.1	n.945C>T		non_coding_transcript_exon_variant	Exon 1 of 3
MIR1302-3	unassigned_transcript_479	n.-62C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR1302-3	ENST00000408128.1	n.11C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000287165	ENST00000666960.2	n.960C>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000291134	ENST00000801450.1	n.421-5464G>A		intron_variant	Intron 4 of 12

Frequencies

GnomAD3 genomes AF: 0.493 AC: 72937 AN: 148014 Hom.: 0 Cov.: 64

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

GnomAD2 exomes AF: 0.319 AC: 55943 AN: 175098 AF XY: 0.310

Gnomad AFR exome AF: 0.346

Gnomad AMR exome AF: 0.356

Gnomad ASJ exome AF: 0.393

Gnomad EAS exome AF: 0.362

Gnomad FIN exome AF: 0.386

Gnomad NFE exome AF: 0.260

Gnomad OTH exome AF: 0.365

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

African (AFR) AF: 0.498 AC: 5017 AN: 10078

American (AMR) AF: 0.493 AC: 16240 AN: 32972

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 5241 AN: 10762

East Asian (EAS) AF: 0.498 AC: 6320 AN: 12692

South Asian (SAS) AF: 0.487 AC: 30024 AN: 61640

European-Finnish (FIN) AF: 0.494 AC: 15128 AN: 30598

Middle Eastern (MID) AF: 0.483 AC: 544 AN: 1126

European-Non Finnish (NFE) AF: 0.487 AC: 86223 AN: 176920

Other (OTH) AF: 0.489 AC: 7517 AN: 15376

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

African (AFR) AF: 0.497 AC: 20361 AN: 40990

American (AMR) AF: 0.494 AC: 7300 AN: 14778

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1638 AN: 3344

East Asian (EAS) AF: 0.498 AC: 2546 AN: 5110

South Asian (SAS) AF: 0.487 AC: 2278 AN: 4676

European-Finnish (FIN) AF: 0.495 AC: 5118 AN: 10332

Middle Eastern (MID) AF: 0.486 AC: 137 AN: 282

European-Non Finnish (NFE) AF: 0.490 AC: 32173 AN: 65682

Other (OTH) AF: 0.492 AC: 1016 AN: 2066

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
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs6542147; hg19: chr2-114340663;