rs2910164

Variant names:

• chr5-160485411-C-G
• rs2910164
• ENST00000517927.1:n.286C>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000517927.1(MIR3142HG):​n.286C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 528,390 control chromosomes in the GnomAD database, including 141,782 homozygotes. 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 0.70 (38097 hom., cov: 31)
  • Exomes 𝑓: 0.74 (103685 hom.)
• Consequence: MIR3142HG ENST00000517927.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57

Genes affected

MIR3142HG (HGNC:51944): (MIR3142 host gene)

MIR146A (HGNC:31533): (microRNA 146a) 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. Some of the targets of the encoded miRNA are the transcripts for tumor necrosis factor, interleukin 1 receptor-associated kinase 1, interleukin 1-beta, TNF receptor-associated factor 6, and complement factor H. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2015]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR146A	NR_029701.1	n.60C>G		non_coding_transcript_exon_variant	Exon 1 of 1
MIR3142HG	NR_132748.1	n.303C>G		non_coding_transcript_exon_variant	Exon 2 of 2
MIR146A	unassigned_transcript_889	n.4C>G		non_coding_transcript_exon_variant	Exon 1 of 1
MIR146A	unassigned_transcript_888	n.*18C>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3142HG	ENST00000517927.1	n.286C>G		non_coding_transcript_exon_variant	Exon 2 of 2	1
MIR146A	ENST00000385201.1	n.60C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
MIR3142HG	ENST00000642173.1	n.189C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106630 AN: 151942 Hom.: 38071 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.687

GnomAD2 exomes AF: 0.713 AC: 175623 AN: 246292 AF XY: 0.719

Gnomad AFR exome AF: 0.598

Gnomad AMR exome AF: 0.694

Gnomad ASJ exome AF: 0.777

Gnomad EAS exome AF: 0.372

Gnomad FIN exome AF: 0.784

Gnomad NFE exome AF: 0.770

Gnomad OTH exome AF: 0.730

GnomAD4 exome AF: 0.737 AC: 277348 AN: 376330 Hom.: 103685 Cov.: 0 AF XY: 0.738 AC XY: 157630 AN XY: 213566

Gnomad4 AFR exome AF: 0.599 AC: 6221 AN: 10394

Gnomad4 AMR exome AF: 0.694 AC: 25001 AN: 36010

Gnomad4 ASJ exome AF: 0.777 AC: 9007 AN: 11590

Gnomad4 EAS exome AF: 0.376 AC: 4886 AN: 13002

Gnomad4 SAS exome AF: 0.727 AC: 48014 AN: 66058

Gnomad4 FIN exome AF: 0.782 AC: 25106 AN: 32104

Gnomad4 NFE exome AF: 0.772 AC: 145312 AN: 188192

Gnomad4 Remaining exome AF: 0.733 AC: 12045 AN: 16422

GnomAD4 genome AF: 0.702 AC: 106701 AN: 152060 Hom.: 38097 Cov.: 31 AF XY: 0.702 AC XY: 52221 AN XY: 74344

Gnomad4 AFR AF: 0.607 AC: 0.606869 AN: 0.606869

Gnomad4 AMR AF: 0.709 AC: 0.708611 AN: 0.708611

Gnomad4 ASJ AF: 0.783 AC: 0.782997 AN: 0.782997

Gnomad4 EAS AF: 0.380 AC: 0.379504 AN: 0.379504

Gnomad4 SAS AF: 0.705 AC: 0.704697 AN: 0.704697

Gnomad4 FIN AF: 0.787 AC: 0.787023 AN: 0.787023

Gnomad4 NFE AF: 0.766 AC: 0.76572 AN: 0.76572

Gnomad4 OTH AF: 0.688 AC: 0.68833 AN: 0.68833

Alfa AF: 0.755 Hom.: 14093

Bravo AF: 0.691

Asia WGS AF: 0.549 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	17
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2910164; hg19: chr5-159912418;