rs13170576

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0872 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.281+6909C>T		intron_variant	Intron 2 of 3

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

Gnomad4 AFR AF: 0.0167

Gnomad4 AMR AF: 0.0345

Gnomad4 ASJ AF: 0.0202

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0257

Gnomad4 FIN AF: 0.0818

Gnomad4 NFE AF: 0.0891

Gnomad4 OTH AF: 0.0425

Alfa AF: 0.0754 Hom.: 278

Bravo AF: 0.0491

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13170576; hg19: chr5-8467174;