ENST00000586905.3:n.37+51990C>T

Variant names:

• chr18-47337751-C-T
• rs3861810
• ENST00000586905.3:n.37+51990C>T

Variant summary

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

The ENST00000586905.3(MIR4527HG):​n.37+51990C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,128 control chromosomes in the GnomAD database, including 45,762 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 (45762 hom., cov: 32)
• Consequence: MIR4527HG ENST00000586905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4527HG	NR_147192.1		n.38+51990C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4527HG	ENST00000586905.3	TSL:1	n.37+51990C>T		intron	N/A
	MIR4527HG	ENST00000598649.1	TSL:3	n.73+51954C>T		intron	N/A
	MIR4527HG	ENST00000833748.1		n.409-20546C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117447 AN: 152010 Hom.: 45710 Cov.: 32

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.773 AC: 117558 AN: 152128 Hom.: 45762 Cov.: 32 AF XY: 0.776 AC XY: 57663 AN XY: 74354

African (AFR) AF: 0.857 AC: 35581 AN: 41506

American (AMR) AF: 0.694 AC: 10606 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2655 AN: 3472

East Asian (EAS) AF: 0.870 AC: 4498 AN: 5170

South Asian (SAS) AF: 0.786 AC: 3780 AN: 4812

European-Finnish (FIN) AF: 0.829 AC: 8773 AN: 10588

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

European-Non Finnish (NFE) AF: 0.722 AC: 49103 AN: 67982

Other (OTH) AF: 0.748 AC: 1578 AN: 2110

Alfa AF: 0.731 Hom.: 53340

Bravo AF: 0.768

Asia WGS AF: 0.816 AC: 2841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.9
DANN	Benign	0.38
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs3861810; hg19: chr18-44864122;