rs67106263

Positions:

• chr6-120015238-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_036098.1(MIR3144):​n.60G>A 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 0.219 in 152,536 control chromosomes in the GnomAD database, including 3,913 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 0.22 (3886 hom., cov: 31)
  • Exomes 𝑓: 0.22 (27 hom.)
• Consequence: MIR3144 NR_036098.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

Genes affected

MIR3144 (HGNC:38331): (microRNA 3144) 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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR3144	NR_036098.1	n.60G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR3144	ENST00000579460.1	n.60G>A		mature_miRNA_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33144 AN: 151418 Hom.: 3875 Cov.: 31

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.218

GnomAD3 exomes AF: 0.229 AC: 1450 AN: 6334 Hom.: 162 AF XY: 0.226 AC XY: 691 AN XY: 3060

Gnomad AFR exome AF: 0.198

Gnomad AMR exome AF: 0.328

Gnomad ASJ exome AF: 0.268

Gnomad EAS exome AF: 0.100

Gnomad SAS exome AF: 0.179

Gnomad NFE exome AF: 0.229

Gnomad OTH exome AF: 0.261

GnomAD4 exome AF: 0.222 AC: 222 AN: 1002 Hom.: 27 Cov.: 0 AF XY: 0.199 AC XY: 112 AN XY: 564

Gnomad4 AFR exome AF: 0.214

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.250

Gnomad4 SAS exome AF: 0.222

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.244

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.219 AC: 33188 AN: 151534 Hom.: 3886 Cov.: 31 AF XY: 0.218 AC XY: 16116 AN XY: 74014

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.215

Alfa AF: 0.210 Hom.: 463

Bravo AF: 0.231

Asia WGS AF: 0.156 AC: 547 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.6
DANN	Benign	0.78
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs67106263; hg19: chr6-120336384;