rs57111412

chr19-53688489-A-G

Variant summary

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

The NR_031573.1(MIR1283-1):n.9A>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 0.149 in 530,934 control chromosomes in the GnomAD database, including 9,479 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 0.19 (4632 hom., cov: 32)
  • Exomes 𝑓: 0.13 (4847 hom.)
• Consequence: MIR1283-1 NR_031573.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

Genes affected

MIR1283-1 (HGNC:35255): (microRNA 1283-1) 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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR1283-1	NR_031573.1	n.9A>G		non_coding_transcript_exon_variant	1/1
LOC107985342	XR_007067332.1	n.356-5540A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR1283-1	ENST00000408494.1	n.9A>G		non_coding_transcript_exon_variant	1/1
	ENST00000710708.1	n.349-1804A>G		intron_variant, non_coding_transcript_variant
	ENST00000710736.1	n.640A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29528 AN: 152006 Hom.: 4623 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.0672

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.0950

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0736

Gnomad OTH AF: 0.182

GnomAD3 exomes AF: 0.149 AC: 36763 AN: 247208 Hom.: 4215 AF XY: 0.146 AC XY: 19499 AN XY: 133902

Gnomad AFR exome AF: 0.430

Gnomad AMR exome AF: 0.159

Gnomad ASJ exome AF: 0.107

Gnomad EAS exome AF: 0.285

Gnomad SAS exome AF: 0.244

Gnomad FIN exome AF: 0.0967

Gnomad NFE exome AF: 0.0737

Gnomad OTH exome AF: 0.116

GnomAD4 exome AF: 0.131 AC: 49657 AN: 378810 Hom.: 4847 Cov.: 0 AF XY: 0.136 AC XY: 29459 AN XY: 215952

Gnomad4 AFR exome AF: 0.421

Gnomad4 AMR exome AF: 0.160

Gnomad4 ASJ exome AF: 0.104

Gnomad4 EAS exome AF: 0.270

Gnomad4 SAS exome AF: 0.235

Gnomad4 FIN exome AF: 0.0978

Gnomad4 NFE exome AF: 0.0729

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.194 AC: 29586 AN: 152124 Hom.: 4632 Cov.: 32 AF XY: 0.196 AC XY: 14570 AN XY: 74382

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.0950

Gnomad4 NFE AF: 0.0736

Gnomad4 OTH AF: 0.185

Alfa AF: 0.124 Hom.: 985

Bravo AF: 0.207

Asia WGS AF: 0.282 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.4
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs57111412; hg19: chr19-54191743; COSMIC: COSV66023764;