rs1560901

Variant names:

• chr18-47340750-A-G
• rs1560901
• ENST00000586905.3:n.37+54989A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-47340750-A-G
• chr18-47340750-A-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+54989A>G 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 152,054 control chromosomes in the GnomAD database, including 45,765 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 (45765 hom., cov: 31)
• Consequence: MIR4527HG ENST00000586905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 1 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+54989A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4527HG	ENST00000586905.3	TSL:1	n.37+54989A>G		intron	N/A
	MIR4527HG	ENST00000598649.1	TSL:3	n.73+54953A>G		intron	N/A
	MIR4527HG	ENST00000833748.1		n.409-17547A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117418 AN: 151934 Hom.: 45713 Cov.: 31

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.773 AC: 117529 AN: 152054 Hom.: 45765 Cov.: 31 AF XY: 0.776 AC XY: 57659 AN XY: 74326

African (AFR) AF: 0.858 AC: 35566 AN: 41462

American (AMR) AF: 0.695 AC: 10593 AN: 15250

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

East Asian (EAS) AF: 0.871 AC: 4506 AN: 5176

South Asian (SAS) AF: 0.786 AC: 3786 AN: 4818

European-Finnish (FIN) AF: 0.828 AC: 8761 AN: 10580

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

European-Non Finnish (NFE) AF: 0.722 AC: 49097 AN: 67982

Other (OTH) AF: 0.750 AC: 1582 AN: 2110

Alfa AF: 0.751 Hom.: 12666

Bravo AF: 0.769

Asia WGS AF: 0.817 AC: 2845 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	5.0
DANN	Benign	0.72
PhyloP100		-0.30

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1560901;

hg19: chr18-44867121;