ENST00000385190.1:n.80_81delTT

Variant names:

• chr19-53725519-CTT-C
• rs10583889
• ENST00000385190.1:n.80_81delTT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000385190.1(MIR516B2):​n.80_81delTT 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 ENST00000385190.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• Publications: 4 publications found

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]

ENSG00000269842 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0838 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000385190.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR516B2	NR_030207.1		n.80_81delTT		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR516B2	ENST00000385190.1	TSL:6	n.80_81delTT		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000269842	ENST00000710708.1		n.585+12420_585+12421delTT		intron	N/A

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

GnomAD2 exomes AF: 0.00391 AC: 948 AN: 242356 AF XY: 0.00260

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 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

African (AFR) AF: 0.0851 AC: 868 AN: 10194

American (AMR) AF: 0.00345 AC: 122 AN: 35318

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11434

East Asian (EAS) AF: 0.0000786 AC: 1 AN: 12730

South Asian (SAS) AF: 0.000963 AC: 62 AN: 64408

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31952

Middle Eastern (MID) AF: 0.0118 AC: 33 AN: 2804

European-Non Finnish (NFE) AF: 0.000192 AC: 35 AN: 182532

Other (OTH) AF: 0.00528 AC: 85 AN: 16104

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

African (AFR) AF: 0.0861 AC: 3578 AN: 41536

American (AMR) AF: 0.00635 AC: 97 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.00145 AC: 7 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10604

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000456 AC: 31 AN: 68006

Other (OTH) AF: 0.0194 AC: 41 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs10583889; hg19: chr19-54228773;