2-113583051-C-G

Variant names:

• chr2-113583051-C-G
• rs7589328
• ENST00000408128.1:n.46G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000408128.1(MIR1302-3):​n.46G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 70)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR1302-3 ENST00000408128.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936
• Publications: 7 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 -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR1302-3	NR_031632.1	n.46G>C		non_coding_transcript_exon_variant	Exon 1 of 1
LOC124907875	XR_007087203.1	n.996G>C		non_coding_transcript_exon_variant	Exon 1 of 2
LOC124907875	XR_007087204.1	n.980G>C		non_coding_transcript_exon_variant	Exon 1 of 3
MIR1302-3	unassigned_transcript_479	n.-27G>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR1302-3	ENST00000408128.1	n.46G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000287165	ENST00000666960.2	n.995G>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000291134	ENST00000801450.1	n.421-5499C>G		intron_variant	Intron 4 of 12

Frequencies

GnomAD3 genomes Cov.: 70

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 334566 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 190518

African (AFR) AF: 0.00 AC: 0 AN: 9100

American (AMR) AF: 0.00 AC: 0 AN: 29880

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10290

East Asian (EAS) AF: 0.00 AC: 0 AN: 11458

South Asian (SAS) AF: 0.00 AC: 0 AN: 60612

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27660

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1096

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 169860

Other (OTH) AF: 0.00 AC: 0 AN: 14610

GnomAD4 genome Cov.: 70

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.94
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7589328; hg19: chr2-114340628;