rs10670323

chr19-53725488-G-GAAAGA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_030207.1(MIR516B2):n.50_54dup 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 0.151 in 152,026 control chromosomes in the GnomAD database, including 2,317 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.15 (2317 hom., cov: 29)
  • Exomes 𝑓: 0.11 (2616 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR516B2 NR_030207.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

MIR516B2 (HGNC:32117): (microRNA 516b-2) 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR516B2	NR_030207.1	n.50_54dup		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR516B2	ENST00000385190.1	n.50_54dup		non_coding_transcript_exon_variant	1/1
	ENST00000710708.1	n.585+12390_585+12394dup		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22932 AN: 151908 Hom.: 2309 Cov.: 29

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0723

Gnomad EAS AF: 0.0644

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.132

GnomAD3 exomes AF: 0.0665 AC: 15644 AN: 235408 Hom.: 1117 AF XY: 0.0640 AC XY: 8139 AN XY: 127198

Gnomad AFR exome AF: 0.202

Gnomad AMR exome AF: 0.0320

Gnomad ASJ exome AF: 0.0346

Gnomad EAS exome AF: 0.0468

Gnomad SAS exome AF: 0.0559

Gnomad FIN exome AF: 0.126

Gnomad NFE exome AF: 0.0576

Gnomad OTH exome AF: 0.0590

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.107 AC: 39550 AN: 369680 Hom.: 2616 Cov.: 0 AF XY: 0.107 AC XY: 22384 AN XY: 209112

Gnomad4 AFR exome AF: 0.296

Gnomad4 AMR exome AF: 0.0511

Gnomad4 ASJ exome AF: 0.0681

Gnomad4 EAS exome AF: 0.0631

Gnomad4 SAS exome AF: 0.112

Gnomad4 FIN exome AF: 0.165

Gnomad4 NFE exome AF: 0.101

Gnomad4 OTH exome AF: 0.106

GnomAD4 genome AF: 0.151 AC: 22982 AN: 152026 Hom.: 2317 Cov.: 29 AF XY: 0.151 AC XY: 11195 AN XY: 74328

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.0725

Gnomad4 ASJ AF: 0.0723

Gnomad4 EAS AF: 0.0641

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.131

Alfa AF: 0.116 Hom.: 240

Bravo AF: 0.150

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10670323; hg19: chr19-54228742;