ENST00000586905.3:n.37+106432T>C

Variant names:

• chr18-47392193-T-C
• rs2060411
• ENST00000586905.3:n.37+106432T>C

Variant summary

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

The ENST00000586905.3(MIR4527HG):​n.37+106432T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 151,698 control chromosomes in the GnomAD database, including 45,198 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 (45198 hom., cov: 28)
• Consequence: MIR4527HG ENST00000586905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4527HG	NR_147192.1	n.38+106432T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4527HG	ENST00000586905.3	n.37+106432T>C		intron_variant	Intron 1 of 2	1
MIR4527HG	ENST00000598649.1	n.73+106396T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116598 AN: 151580 Hom.: 45147 Cov.: 28

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.769 AC: 116709 AN: 151698 Hom.: 45198 Cov.: 28 AF XY: 0.772 AC XY: 57199 AN XY: 74086

African (AFR) AF: 0.843 AC: 34815 AN: 41314

American (AMR) AF: 0.693 AC: 10579 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2654 AN: 3470

East Asian (EAS) AF: 0.891 AC: 4589 AN: 5148

South Asian (SAS) AF: 0.796 AC: 3798 AN: 4770

European-Finnish (FIN) AF: 0.811 AC: 8506 AN: 10492

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49210 AN: 67940

Other (OTH) AF: 0.748 AC: 1572 AN: 2102

Alfa AF: 0.734 Hom.: 60202

Bravo AF: 0.765

Asia WGS AF: 0.820 AC: 2852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.7
DANN	Benign	0.77
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs2060411; hg19: chr18-44918564;