18-47530300-G-A

Variant names:

• chr18-47530300-G-A
• rs6507763
• ENST00000586905.3:n.38-44296G>A

Variant summary

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

The ENST00000586905.3(MIR4527HG):​n.38-44296G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,160 control chromosomes in the GnomAD database, including 2,650 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 0.18 (2650 hom., cov: 33)
• Consequence: MIR4527HG ENST00000586905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.78
• Publications: 3 publications found

Genes affected

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

ENSG00000261307 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 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.39-44296G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4527HG	ENST00000586905.3	TSL:1	n.38-44296G>A		intron	N/A
	ENSG00000261307	ENST00000565127.1	TSL:4	n.276-15114G>A		intron	N/A
	MIR4527HG	ENST00000598649.1	TSL:3	n.74-31434G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27483 AN: 152042 Hom.: 2645 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.181 AC: 27501 AN: 152160 Hom.: 2650 Cov.: 33 AF XY: 0.183 AC XY: 13619 AN XY: 74386

African (AFR) AF: 0.211 AC: 8748 AN: 41518

American (AMR) AF: 0.156 AC: 2379 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3466

East Asian (EAS) AF: 0.108 AC: 557 AN: 5178

South Asian (SAS) AF: 0.154 AC: 740 AN: 4814

European-Finnish (FIN) AF: 0.270 AC: 2857 AN: 10588

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11188 AN: 67990

Other (OTH) AF: 0.151 AC: 319 AN: 2112

Alfa AF: 0.168 Hom.: 1275

Bravo AF: 0.171

Asia WGS AF: 0.126 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	16
DANN	Benign	0.68
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs6507763; hg19: chr18-45056671;