chr19-53742534-G-A

Variant names:

• chr19-53742534-G-A
• rs56013413
• ENST00000385126.1:n.23G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 8 publications found

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]

ENSG00000269842 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000385126.1. 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
	MIR520H	NR_030215.1		n.23G>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR520H	ENST00000385126.1	TSL:6	n.23G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000269842	ENST00000710696.1		n.791+267G>A		intron	N/A
	ENSG00000269842	ENST00000710698.1		n.147+267G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0834 AC: 12691 AN: 152084 Hom.: 1044 Cov.: 32

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

GnomAD2 exomes AF: 0.0424 AC: 10479 AN: 247214 AF XY: 0.0391

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 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.: 0 AF XY: 0.0349 AC XY: 7548 AN XY: 216540

African (AFR) AF: 0.221 AC: 2284 AN: 10320

American (AMR) AF: 0.0235 AC: 839 AN: 35740

Ashkenazi Jewish (ASJ) AF: 0.0243 AC: 284 AN: 11690

East Asian (EAS) AF: 0.000228 AC: 3 AN: 13164

South Asian (SAS) AF: 0.0242 AC: 1595 AN: 66042

European-Finnish (FIN) AF: 0.0433 AC: 1398 AN: 32292

Middle Eastern (MID) AF: 0.0486 AC: 138 AN: 2840

European-Non Finnish (NFE) AF: 0.0349 AC: 6676 AN: 191560

Other (OTH) AF: 0.0402 AC: 670 AN: 16648

GnomAD4 genome AF: 0.0836 AC: 12717 AN: 152202 Hom.: 1047 Cov.: 32 AF XY: 0.0807 AC XY: 6004 AN XY: 74426

African (AFR) AF: 0.216 AC: 8974 AN: 41486

American (AMR) AF: 0.0434 AC: 663 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0291 AC: 101 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0240 AC: 116 AN: 4832

European-Finnish (FIN) AF: 0.0452 AC: 479 AN: 10606

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0327 AC: 2222 AN: 68020

Other (OTH) AF: 0.0676 AC: 143 AN: 2114

Alfa AF: 0.0550 Hom.: 246

Bravo AF: 0.0892

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.38
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs56013413; hg19: chr19-54245788;