rs480213

Variant names:

• chr11-82093529-A-G
• rs480213
• ENST00000500502.5:n.813+2932T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000500502.5(MIR4300HG):​n.813+2932T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0876 in 152,220 control chromosomes in the GnomAD database, including 715 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 0.088 (715 hom., cov: 32)
• Consequence: MIR4300HG ENST00000500502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315
• Publications: 2 publications found

Genes affected

MIR4300HG (HGNC:52003): (MIR4300 host gene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500502.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4300HG	NR_120571.1		n.813+2932T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4300HG	ENST00000500502.5	TSL:1	n.813+2932T>C		intron	N/A
	MIR4300HG	ENST00000530896.6	TSL:3	n.345+6445T>C		intron	N/A
	MIR4300HG	ENST00000653173.1		n.418+6445T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0874 AC: 13290 AN: 152102 Hom.: 708 Cov.: 32

Gnomad AFR AF: 0.0393

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.0507

Gnomad FIN AF: 0.0763

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0876 AC: 13328 AN: 152220 Hom.: 715 Cov.: 32 AF XY: 0.0861 AC XY: 6412 AN XY: 74440

African (AFR) AF: 0.0397 AC: 1649 AN: 41552

American (AMR) AF: 0.145 AC: 2223 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0882 AC: 306 AN: 3468

East Asian (EAS) AF: 0.00367 AC: 19 AN: 5178

South Asian (SAS) AF: 0.0511 AC: 247 AN: 4832

European-Finnish (FIN) AF: 0.0763 AC: 809 AN: 10606

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7694 AN: 67986

Other (OTH) AF: 0.107 AC: 226 AN: 2112

Alfa AF: 0.107 Hom.: 169

Bravo AF: 0.0936

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.60
PhyloP100		0.32
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs480213;

hg19: chr11-81804571;