ENST00000652260.1:n.282-1907A>G

Variant names:

• chr5-8477167-A-G
• rs341880
• ENST00000652260.1:n.282-1907A>G

Variant summary

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

The ENST00000652260.1(MIR4458HG):​n.282-1907A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,176 control chromosomes in the GnomAD database, including 52,663 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 0.82 (52663 hom., cov: 33)
• Consequence: MIR4458HG ENST00000652260.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.935 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4458HG	ENST00000652260.1		n.282-1907A>G		intron	N/A
	MIR4458HG	ENST00000721170.1		n.101-1907A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124766 AN: 152058 Hom.: 52670 Cov.: 33

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.820 AC: 124794 AN: 152176 Hom.: 52663 Cov.: 33 AF XY: 0.817 AC XY: 60822 AN XY: 74434

African (AFR) AF: 0.642 AC: 26640 AN: 41468

American (AMR) AF: 0.722 AC: 11037 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 3271 AN: 3472

East Asian (EAS) AF: 0.639 AC: 3303 AN: 5166

South Asian (SAS) AF: 0.873 AC: 4214 AN: 4828

European-Finnish (FIN) AF: 0.892 AC: 9463 AN: 10612

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 64022 AN: 68026

Other (OTH) AF: 0.823 AC: 1739 AN: 2112

Alfa AF: 0.721 Hom.: 7153

Bravo AF: 0.792

Asia WGS AF: 0.719 AC: 2500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.56
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs341880; hg19: chr5-8477280;