rs1594887

Variant names:

• chr18-47365998-G-A
• rs1594887
• ENST00000586905.3:n.37+80237G>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+80237G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,114 control chromosomes in the GnomAD database, including 41,554 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 0.74 (41554 hom., cov: 32)
• Consequence: MIR4527HG ENST00000586905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4527HG	NR_147192.1	n.38+80237G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4527HG	ENST00000586905.3	n.37+80237G>A		intron_variant	Intron 1 of 2	1
MIR4527HG	ENST00000598649.1	n.73+80201G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112156 AN: 151996 Hom.: 41507 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.738 AC: 112261 AN: 152114 Hom.: 41554 Cov.: 32 AF XY: 0.743 AC XY: 55242 AN XY: 74392

African (AFR) AF: 0.734 AC: 30461 AN: 41478

American (AMR) AF: 0.679 AC: 10383 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2657 AN: 3472

East Asian (EAS) AF: 0.885 AC: 4574 AN: 5168

South Asian (SAS) AF: 0.786 AC: 3792 AN: 4824

European-Finnish (FIN) AF: 0.829 AC: 8768 AN: 10576

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.722 AC: 49112 AN: 67994

Other (OTH) AF: 0.726 AC: 1533 AN: 2112

Alfa AF: 0.729 Hom.: 155118

Bravo AF: 0.728

Asia WGS AF: 0.816 AC: 2839 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	0.12
DANN	Benign	0.33
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1594887; hg19: chr18-44892369;