5-8468031-A-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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
MIR4458HG	ENST00000721170.1	n.100+8056A>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

African (AFR) AF: 0.651 AC: 27006 AN: 41462

American (AMR) AF: 0.723 AC: 11042 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 3269 AN: 3470

East Asian (EAS) AF: 0.639 AC: 3289 AN: 5150

South Asian (SAS) AF: 0.876 AC: 4215 AN: 4814

European-Finnish (FIN) AF: 0.892 AC: 9432 AN: 10578

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 64027 AN: 68018

Other (OTH) AF: 0.825 AC: 1745 AN: 2114

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
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs341892; hg19: chr5-8468144;