rs34059726

Variant names:

• chr20-63178555-G-T
• rs34059726
• ENST00000384866.1:n.56G>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000384866.1(MIR124-3):​n.56G>T variant causes a non coding transcript exon change. 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: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR124-3 ENST00000384866.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.85
• Publications: 11 publications found

Genes affected

MIR124-3 (HGNC:31504): (microRNA 124-3) 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]

ENSG00000231977 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR124-3	NR_029670.1	n.56G>T		non_coding_transcript_exon_variant	Exon 1 of 1
MIR124-3	unassigned_transcript_3480	n.4G>T		non_coding_transcript_exon_variant	Exon 1 of 1
MIR124-3	unassigned_transcript_3479	n.*20G>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR124-3	ENST00000384866.1	n.56G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000231977	ENST00000423020.2	n.188+2161C>A		intron_variant	Intron 1 of 1	4
ENSG00000231977	ENST00000726823.1	n.114-11405C>A		intron_variant	Intron 1 of 1
ENSG00000231977	ENST00000726824.1	n.42+1041C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 361024 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 206942

African (AFR) AF: 0.00 AC: 0 AN: 7496

American (AMR) AF: 0.00 AC: 0 AN: 34442

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11118

East Asian (EAS) AF: 0.00 AC: 0 AN: 10476

South Asian (SAS) AF: 0.00 AC: 0 AN: 64160

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31274

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2590

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 183642

Other (OTH) AF: 0.00 AC: 0 AN: 15826

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	21
DANN	Benign	0.97
PhyloP100		6.9

Splicing

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

Other links and lift over

dbSNP: rs34059726; hg19: chr20-61809907;