rs341893

chr5-8467787-A-Cchr5-8467787-A-T

Variant summary

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

The ENST00000652260.1(MIR4458HG):n.281+7635A>C 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 0.822 in 152,182 control chromosomes in the GnomAD database, including 52,885 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 (52885 hom., cov: 33)
• Consequence: MIR4458HG ENST00000652260.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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=-0.94).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4458HG	ENST00000652260.1	n.281+7635A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125077 AN: 152064 Hom.: 52889 Cov.: 33

Gnomad AFR AF: 0.649

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: 0.822 AC: 125109 AN: 152182 Hom.: 52885 Cov.: 33 AF XY: 0.819 AC XY: 60960 AN XY: 74410

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.942

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.875

Gnomad4 FIN AF: 0.892

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.826

Alfa AF: 0.922 Hom.: 100111

Bravo AF: 0.794

Asia WGS AF: 0.722 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.70
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs341893; hg19: chr5-8467900;