rs4939797

Variant names:

• chr18-47507115-G-A
• rs4939797
• ENST00000586905.3:n.38-67481G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-47507115-G-A
• chr18-47507115-G-T

Variant summary

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

The ENST00000586905.3(MIR4527HG):​n.38-67481G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,056 control chromosomes in the GnomAD database, including 9,760 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 0.34 (9760 hom., cov: 32)
• Consequence: MIR4527HG ENST00000586905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 1 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=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 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.39-67481G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4527HG	ENST00000586905.3	TSL:1	n.38-67481G>A		intron	N/A
	ENSG00000261307	ENST00000565127.1	TSL:4	n.69-4625G>A		intron	N/A
	MIR4527HG	ENST00000598649.1	TSL:3	n.74-54619G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51617 AN: 151938 Hom.: 9761 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.0502

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.339 AC: 51612 AN: 152056 Hom.: 9760 Cov.: 32 AF XY: 0.332 AC XY: 24679 AN XY: 74330

African (AFR) AF: 0.214 AC: 8868 AN: 41478

American (AMR) AF: 0.338 AC: 5162 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1641 AN: 3470

East Asian (EAS) AF: 0.0501 AC: 259 AN: 5172

South Asian (SAS) AF: 0.291 AC: 1396 AN: 4804

European-Finnish (FIN) AF: 0.330 AC: 3486 AN: 10558

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29501 AN: 67970

Other (OTH) AF: 0.391 AC: 826 AN: 2112

Alfa AF: 0.403 Hom.: 36707

Bravo AF: 0.334

Asia WGS AF: 0.174 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.8
DANN	Benign	0.81
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs4939797; hg19: chr18-45033486;