5-8477167-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4458HG	ENST00000652260.1	n.282-1907A>G		intron_variant	Intron 2 of 3

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

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.942

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.892

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.823

Alfa AF: 0.807 Hom.: 4239

Bravo AF: 0.792

Asia WGS AF: 0.719 AC: 2500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs341880; hg19: chr5-8477280;