rs10583889

Positions:

• chr19-53725519-CTT-C
• chr19-53725519-CTT-CTTT

Variant summary

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

The NR_030207.1(MIR516B2):​n.80_81del 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 0.00955 in 519,700 control chromosomes in the GnomAD database, including 218 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.025 (169 hom., cov: 32)
  • Exomes 𝑓: 0.0033 (49 hom.)
• Consequence: MIR516B2 NR_030207.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

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 = 0.0838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR516B2	NR_030207.1	n.80_81del		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR516B2	ENST00000385190.1	n.80_81del		non_coding_transcript_exon_variant	1/1
	ENST00000710708.1	n.585+12420_585+12421del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0246 AC: 3736 AN: 152106 Hom.: 167 Cov.: 32

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00642

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000456

Gnomad OTH AF: 0.0196

GnomAD3 exomes AF: 0.00391 AC: 948 AN: 242356 Hom.: 36 AF XY: 0.00260 AC XY: 341 AN XY: 131228

Gnomad AFR exome AF: 0.0576

Gnomad AMR exome AF: 0.00175

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000111

Gnomad SAS exome AF: 0.000485

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000135

Gnomad OTH exome AF: 0.00152

GnomAD4 exome AF: 0.00328 AC: 1206 AN: 367476 Hom.: 49 AF XY: 0.00243 AC XY: 504 AN XY: 207750

Gnomad4 AFR exome AF: 0.0851

Gnomad4 AMR exome AF: 0.00345

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000786

Gnomad4 SAS exome AF: 0.000963

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000192

Gnomad4 OTH exome AF: 0.00528

GnomAD4 genome AF: 0.0247 AC: 3756 AN: 152224 Hom.: 169 Cov.: 32 AF XY: 0.0236 AC XY: 1758 AN XY: 74426

Gnomad4 AFR AF: 0.0861

Gnomad4 AMR AF: 0.00635

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000456

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0132 Hom.: 14

Bravo AF: 0.0279

Asia WGS AF: 0.00924 AC: 32 AN: 3478

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: rs10583889; hg19: chr19-54228773;