ENST00000652260.1:n.281+7635A>C

Variant names:

• chr5-8467787-A-C
• rs341893
• ENST00000652260.1:n.281+7635A>C

Variant summary

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

The ENST00000652260.1(MIR4458HG):​n.281+7635A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,182 control chromosomes in the GnomAD database, including 52,885 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 (52885 hom., cov: 33)
• Consequence: MIR4458HG ENST00000652260.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 3 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=-0.94).
• 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4458HG	ENST00000652260.1		n.281+7635A>C		intron	N/A
	MIR4458HG	ENST00000721170.1		n.100+7812A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125077 AN: 152064 Hom.: 52889 Cov.: 33

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.822 AC: 125109 AN: 152182 Hom.: 52885 Cov.: 33 AF XY: 0.819 AC XY: 60960 AN XY: 74410

African (AFR) AF: 0.649 AC: 26932 AN: 41486

American (AMR) AF: 0.723 AC: 11048 AN: 15286

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

East Asian (EAS) AF: 0.639 AC: 3299 AN: 5164

South Asian (SAS) AF: 0.875 AC: 4224 AN: 4826

European-Finnish (FIN) AF: 0.892 AC: 9459 AN: 10608

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 64027 AN: 68024

Other (OTH) AF: 0.826 AC: 1742 AN: 2110

Alfa AF: 0.900 Hom.: 232774

Bravo AF: 0.794

Asia WGS AF: 0.722 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.70
DANN	Benign	0.52
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs341893; hg19: chr5-8467900;