rs10488825

Variant names:

• chr11-82299830-G-A
• rs10488825
• ENST00000500502.5:n.431+50096C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-82299830-G-A
• chr11-82299830-G-T

Variant summary

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

The ENST00000500502.5(MIR4300HG):​n.431+50096C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 151,984 control chromosomes in the GnomAD database, including 920 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 0.11 (920 hom., cov: 32)
• Consequence: MIR4300HG ENST00000500502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 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.431+50096C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4300HG	ENST00000500502.5	TSL:1	n.431+50096C>T		intron	N/A
	MIR4300HG	ENST00000532217.1	TSL:5	n.557+56682C>T		intron	N/A
	MIR4300HG	ENST00000653173.1		n.184+56682C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16012 AN: 151866 Hom.: 919 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.0940

Gnomad ASJ AF: 0.0939

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0373

Gnomad FIN AF: 0.0571

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.105 AC: 16021 AN: 151984 Hom.: 920 Cov.: 32 AF XY: 0.103 AC XY: 7619 AN XY: 74304

African (AFR) AF: 0.139 AC: 5769 AN: 41468

American (AMR) AF: 0.0938 AC: 1430 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0939 AC: 326 AN: 3470

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5176

South Asian (SAS) AF: 0.0369 AC: 178 AN: 4824

European-Finnish (FIN) AF: 0.0571 AC: 605 AN: 10598

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7225 AN: 67888

Other (OTH) AF: 0.113 AC: 237 AN: 2106

Alfa AF: 0.0622 Hom.: 79

Bravo AF: 0.111

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.9
DANN	Benign	0.72
PhyloP100		-0.0050

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: rs10488825;

hg19: chr11-82010872;