18-47392956-T-C

Variant names:

• chr18-47392956-T-C
• rs1893784
• ENST00000586905.3:n.37+107195T>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+107195T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,034 control chromosomes in the GnomAD database, including 6,044 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 0.26 (6044 hom., cov: 32)
• Consequence: MIR4527HG ENST00000586905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 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+107195T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4527HG	ENST00000586905.3	TSL:1	n.37+107195T>C		intron	N/A
	MIR4527HG	ENST00000598649.1	TSL:3	n.73+107159T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.263 AC: 40027 AN: 151918 Hom.: 6044 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.263 AC: 40026 AN: 152034 Hom.: 6044 Cov.: 32 AF XY: 0.267 AC XY: 19820 AN XY: 74306

African (AFR) AF: 0.110 AC: 4582 AN: 41492

American (AMR) AF: 0.302 AC: 4609 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1219 AN: 3464

East Asian (EAS) AF: 0.342 AC: 1761 AN: 5156

South Asian (SAS) AF: 0.260 AC: 1248 AN: 4804

European-Finnish (FIN) AF: 0.369 AC: 3903 AN: 10566

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.315 AC: 21405 AN: 67972

Other (OTH) AF: 0.296 AC: 624 AN: 2108

Alfa AF: 0.260 Hom.: 1932

Bravo AF: 0.256

Asia WGS AF: 0.266 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.84
DANN	Benign	0.53
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1893784; hg19: chr18-44919327;