ENST00000652260.1:n.281+6909C>T

Variant names:

• chr5-8467061-C-T
• rs13170576
• ENST00000652260.1:n.281+6909C>T

Variant summary

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

The ENST00000652260.1(MIR4458HG):​n.281+6909C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0555 in 152,200 control chromosomes in the GnomAD database, including 334 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 0.056 (334 hom., cov: 32)
• Consequence: MIR4458HG ENST00000652260.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427
• Publications: 1 publications found

Genes affected

MIR4458HG (HGNC:49008): (MIR4458 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0872 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652260.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4458HG	ENST00000652260.1		n.281+6909C>T		intron	N/A
	MIR4458HG	ENST00000721170.1		n.100+7086C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0556 AC: 8455 AN: 152082 Hom.: 335 Cov.: 32

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0346

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.0818

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0891

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0555 AC: 8451 AN: 152200 Hom.: 334 Cov.: 32 AF XY: 0.0540 AC XY: 4015 AN XY: 74412

African (AFR) AF: 0.0167 AC: 693 AN: 41526

American (AMR) AF: 0.0345 AC: 528 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3468

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5184

South Asian (SAS) AF: 0.0257 AC: 124 AN: 4822

European-Finnish (FIN) AF: 0.0818 AC: 865 AN: 10578

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0891 AC: 6059 AN: 68006

Other (OTH) AF: 0.0425 AC: 90 AN: 2116

Alfa AF: 0.0650 Hom.: 350

Bravo AF: 0.0491

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.71
PhyloP100		-0.43

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: rs13170576;

hg19: chr5-8467174;