18-47390003-G-A

Variant names:

• chr18-47390003-G-A
• rs892583
• ENST00000586905.3:n.37+104242G>A

Variant summary

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

The ENST00000586905.3(MIR4527HG):​n.37+104242G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,066 control chromosomes in the GnomAD database, including 45,925 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 0.77 (45925 hom., cov: 31)
• Consequence: MIR4527HG ENST00000586905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135
• Publications: 2 publications found

Genes affected

MIR4527HG (HGNC:31724): (MIR4527 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000586905.3. 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
	MIR4527HG	NR_147192.1		n.38+104242G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4527HG	ENST00000586905.3	TSL:1	n.37+104242G>A		intron	N/A
	MIR4527HG	ENST00000598649.1	TSL:3	n.73+104206G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117621 AN: 151948 Hom.: 45877 Cov.: 31

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.750

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.774 AC: 117729 AN: 152066 Hom.: 45925 Cov.: 31 AF XY: 0.777 AC XY: 57722 AN XY: 74334

African (AFR) AF: 0.861 AC: 35707 AN: 41490

American (AMR) AF: 0.695 AC: 10619 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2654 AN: 3472

East Asian (EAS) AF: 0.891 AC: 4608 AN: 5170

South Asian (SAS) AF: 0.788 AC: 3791 AN: 4812

European-Finnish (FIN) AF: 0.811 AC: 8577 AN: 10576

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49198 AN: 67958

Other (OTH) AF: 0.753 AC: 1587 AN: 2108

Alfa AF: 0.733 Hom.: 6864

Bravo AF: 0.771

Asia WGS AF: 0.818 AC: 2845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	11
DANN	Benign	0.58
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs892583; hg19: chr18-44916374;