Genetic Variant MIR516B1:n.76G>A (chr19-53736920-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000385211.3(MIR516B1):n.76G>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 0.00939 in 532,994 control chromosomes in the GnomAD database, including 237 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 0.0073 ( 39 hom., cov: 32)

Exomes 𝑓: 0.010 ( 198 hom. )

Consequence

MIR516B1
ENST00000385211.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.599

Publications

6 publications found

Variant links:

COSMIC-nc: COSV66046291

Genes affected

MIR516B1 (HGNC:32122): (microRNA 516b-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]

MIR516B1 links:

ENSG00000269842 (HGNC:):

ENSG00000269842 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR516B1	NR_030212.1 link	n.76G>A	non_coding_transcript_exon_variant	Exon 1 of 1
MIR516B1	unassigned_transcript_3377	n.16G>A	splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 1
MIR516B1	unassigned_transcript_3376	n.*39G>A	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR516B1	ENST00000385211.3 link	n.76G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000269842	ENST00000710696.1 link	n.325+321G>A	intron_variant	Intron 3 of 11
ENSG00000269842	ENST00000710708.1 link	n.586-9283G>A	intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes

AF:

0.00726

AC:

1105

AN:

152140

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000700

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0560

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0383

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000206

Gnomad OTH

AF:

0.00191

GnomAD2 exomes

AF:

0.0150

AC:

3749

AN:

249634

AF XY:

0.0114

show subpopulations

Gnomad AFR exome

AF:

0.000556

Gnomad AMR exome

AF:

0.0912

Gnomad ASJ exome

AF:

0.000299

Gnomad EAS exome

AF:

0.0321

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000442

Gnomad OTH exome

AF:

0.00834

GnomAD4 exome

AF:

0.0102

AC:

3891

AN:

380736

Hom.:

198

Cov.:

AF XY:

0.00773

AC XY:

1677

AN XY:

216840

show subpopulations

African (AFR)

AF:

0.000478

AC:

AN:

10464

American (AMR)

AF:

0.0917

AC:

3266

AN:

35600

Ashkenazi Jewish (ASJ)

AF:

0.000341

AC:

AN:

11732

East Asian (EAS)

AF:

0.0390

AC:

511

AN:

13108

South Asian (SAS)

AF:

0.000602

AC:

AN:

66454

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32312

Middle Eastern (MID)

AF:

0.000351

AC:

AN:

2850

European-Non Finnish (NFE)

AF:

0.0000835

AC:

AN:

191532

Other (OTH)

AF:

0.00288

AC:

AN:

16684

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.410

Heterozygous variant carriers

139

279

418

558

697

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

140

210

280

350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00730

AC:

1112

AN:

152258

Hom.:

Cov.:

AF XY:

0.00826

AC XY:

615

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.000698

AC:

AN:

41550

American (AMR)

AF:

0.0563

AC:

861

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.0382

AC:

198

AN:

5184

South Asian (SAS)

AF:

0.00124

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10616

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000206

AC:

AN:

68012

Other (OTH)

AF:

0.00189

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

100

149

199

249

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00297

Hom.:

Bravo

AF:

0.0110

Asia WGS

AF:

0.0200

AC:

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

3.1

(source)

DANN

Benign

0.46

PhyloP100

-0.60

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over