rs10488825

chr11-82299830-G-Achr11-82299830-G-T

Variant summary

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

The NR_120571.1(MIR4300HG):n.431+50096C>T 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 0.105 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 NR_120571.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR4300HG	NR_120571.1	n.431+50096C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4300HG	ENST00000532217.1	n.557+56682C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0938

Gnomad4 ASJ AF: 0.0939

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0369

Gnomad4 FIN AF: 0.0571

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0600 Hom.: 71

Bravo AF: 0.111

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.9
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488825; hg19: chr11-82010872;