rs9326439

chr11-82421556-G-A

Variant summary

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

The ENST00000532217.1(MIR4300HG):n.441-64928C>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 0.82 in 148,232 control chromosomes in the GnomAD database, including 51,319 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 (51319 hom., cov: 30)
• Consequence: MIR4300HG ENST00000532217.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4300HG	ENST00000532217.1	n.441-64928C>T		intron_variant, non_coding_transcript_variant		5
MIR4300HG	ENST00000668951.1	n.129+50386C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.820 AC: 121391 AN: 148124 Hom.: 51268 Cov.: 30

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.837

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.820 AC: 121502 AN: 148232 Hom.: 51319 Cov.: 30 AF XY: 0.808 AC XY: 58412 AN XY: 72316

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.858

Gnomad4 OTH AF: 0.810

Alfa AF: 0.837 Hom.: 17800

Bravo AF: 0.823

Asia WGS AF: 0.580 AC: 2012 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.89
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9326439; hg19: chr11-82132598;