Genetic Variant ENST00000385126.1:n.23G>A (chr19-53742534-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000385126.1(MIR520H):n.23G>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 0.05 in 532,498 control chromosomes in the GnomAD database, including 1,489 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 0.084 ( 1047 hom., cov: 32)

Exomes 𝑓: 0.037 ( 442 hom. )

Consequence

MIR520H
ENST00000385126.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.365

Variant links:

Genes affected

MIR520H (HGNC:32125): (microRNA 520h) 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]

MIR520H links:

ENSG00000269842 (HGNC:):

ENSG00000269842 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR520H	NR_030215.1 link	n.23G>A	non_coding_transcript_exon_variant	Exon 1 of 1
LOC124904765	XR_007067333.1 link	n.281+267G>A	intron_variant	Intron 1 of 4
LOC124904765	XR_007067334.1 link	n.373+267G>A	intron_variant	Intron 2 of 5
MIR520H	unassigned_transcript_3382	n.-32G>A	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR520H	ENST00000385126.1 link	n.23G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000269842	ENST00000710696.1 link	n.791+267G>A	intron_variant	Intron 7 of 11
ENSG00000269842	ENST00000710698.1 link	n.147+267G>A	intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes

AF:

0.0834

AC:

12691

AN:

152084

Hom.:

1044

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.00769

Gnomad AMR

AF:

0.0434

Gnomad ASJ

AF:

0.0291

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0240

Gnomad FIN

AF:

0.0452

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0327

Gnomad OTH

AF:

0.0684

GnomAD3 exomes

AF:

0.0424

AC:

10479

AN:

247214

Hom.:

541

AF XY:

0.0391

AC XY:

5229

AN XY:

133746

show subpopulations

Gnomad AFR exome

AF:

0.224

Gnomad AMR exome

AF:

0.0241

Gnomad ASJ exome

AF:

0.0256

Gnomad EAS exome

AF:

0.000443

Gnomad SAS exome

AF:

0.0243

Gnomad FIN exome

AF:

0.0461

Gnomad NFE exome

AF:

0.0347

Gnomad OTH exome

AF:

0.0324

GnomAD4 exome

AF:

0.0365

AC:

13887

AN:

380296

Hom.:

442

Cov.:

AF XY:

0.0349

AC XY:

7548

AN XY:

216540

show subpopulations

Gnomad4 AFR exome

AF:

0.221

Gnomad4 AMR exome

AF:

0.0235

Gnomad4 ASJ exome

AF:

0.0243

Gnomad4 EAS exome

AF:

0.000228

Gnomad4 SAS exome

AF:

0.0242

Gnomad4 FIN exome

AF:

0.0433

Gnomad4 NFE exome

AF:

0.0349

Gnomad4 OTH exome

AF:

0.0402

GnomAD4 genome

AF:

0.0836

AC:

12717

AN:

152202

Hom.:

1047

Cov.:

AF XY:

0.0807

AC XY:

6004

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.216

Gnomad4 AMR

AF:

0.0434

Gnomad4 ASJ

AF:

0.0291

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.0240

Gnomad4 FIN

AF:

0.0452

Gnomad4 NFE

AF:

0.0327

Gnomad4 OTH

AF:

0.0676

Alfa

AF:

0.0550

Hom.:

246

Bravo

AF:

0.0892

Asia WGS

AF:

0.0260

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.3

DANN

Benign

0.38

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over