rs10488824

Variant names:

• chr11-82289597-C-G
• rs10488824
• ENST00000500502.5:n.431+60329G>C

Variant summary

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

The ENST00000500502.5(MIR4300HG):​n.431+60329G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,994 control chromosomes in the GnomAD database, including 5,024 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 0.25 (5024 hom., cov: 32)
• Consequence: MIR4300HG ENST00000500502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4300HG	NR_120571.1	n.431+60329G>C		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4300HG	ENST00000500502.5	n.431+60329G>C		intron_variant	Intron 3 of 7	1
MIR4300HG	ENST00000532217.1	n.557+66915G>C		intron_variant	Intron 4 of 4	5
MIR4300HG	ENST00000653173.1	n.184+66915G>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37909 AN: 151876 Hom.: 5029 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.249 AC: 37899 AN: 151994 Hom.: 5024 Cov.: 32 AF XY: 0.251 AC XY: 18646 AN XY: 74282

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.247

Alfa AF: 0.252 Hom.: 629

Bravo AF: 0.239

Asia WGS AF: 0.287 AC: 1001 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	15
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488824; hg19: chr11-82000639;