ENST00000652260.1:n.356-288T>C

Variant names:

• chr5-8485800-T-C
• rs10512966
• ENST00000652260.1:n.356-288T>C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000652260.1(MIR4458HG):​n.356-288T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00732 in 152,284 control chromosomes in the GnomAD database, including 9 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 0.0073 (9 hom., cov: 32)
• Consequence: MIR4458HG ENST00000652260.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BS2: High Homozygotes in GnomAd4 at 9 gene

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.356-288T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.00732 AC: 1114 AN: 152166 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.00183

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.00151

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00310

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.00287

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

GnomAD4 genome AF: 0.00732 AC: 1114 AN: 152284 Hom.: 9 Cov.: 32 AF XY: 0.00764 AC XY: 569 AN XY: 74464

Gnomad4 AFR AF: 0.00183

Gnomad4 AMR AF: 0.00151

Gnomad4 ASJ AF: 0.00519

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00311

Gnomad4 FIN AF: 0.0184

Gnomad4 NFE AF: 0.0110

Gnomad4 OTH AF: 0.00284

Alfa AF: 0.00974 Hom.: 0

Bravo AF: 0.00591

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.8
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512966; hg19: chr5-8485913;