rs13170576

chr5-8467061-C-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4458HG	ENST00000652260.1	n.281+6909C>T		intron_variant, non_coding_transcript_variant

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;