5-8468031-A-T

Variant names:

• chr5-8468031-A-T
• rs341892
• ENST00000652260.1:n.281+7879A>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652260.1(MIR4458HG):​n.281+7879A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,084 control chromosomes in the GnomAD database, including 52,927 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 (52927 hom., cov: 31)
• Consequence: MIR4458HG ENST00000652260.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

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=-1.02).
• 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.281+7879A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125099 AN: 151966 Hom.: 52931 Cov.: 31

Gnomad AFR AF: 0.652

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: 0.823 AC: 125132 AN: 152084 Hom.: 52927 Cov.: 31 AF XY: 0.820 AC XY: 60933 AN XY: 74340

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.942

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.892

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.825

Alfa AF: 0.874 Hom.: 7353

Bravo AF: 0.795

Asia WGS AF: 0.723 AC: 2513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs341892; hg19: chr5-8468144;