rs9326439

Variant names:

• chr11-82421556-G-A
• rs9326439
• ENST00000532217.1:n.441-64928C>T

Variant summary

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

The ENST00000532217.1(MIR4300HG):​n.441-64928C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• 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=-0.89).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4300HG	ENST00000532217.1	n.441-64928C>T		intron_variant	Intron 3 of 4	5
MIR4300HG	ENST00000668951.1	n.129+50386C>T		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.875 AC: 35166 AN: 40198

American (AMR) AF: 0.766 AC: 11429 AN: 14918

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2755 AN: 3382

East Asian (EAS) AF: 0.321 AC: 1624 AN: 5052

South Asian (SAS) AF: 0.710 AC: 3290 AN: 4636

European-Finnish (FIN) AF: 0.727 AC: 7326 AN: 10082

Middle Eastern (MID) AF: 0.822 AC: 235 AN: 286

European-Non Finnish (NFE) AF: 0.858 AC: 57361 AN: 66834

Other (OTH) AF: 0.810 AC: 1666 AN: 2058

Alfa AF: 0.837 Hom.: 20845

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
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs9326439; hg19: chr11-82132598;