rs208824

Variant names:

• chr15-89384329-T-C
• rs208824
• ENST00000536780.6:n.1038-3488T>C

Variant summary

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

The ENST00000536780.6(MIR9-3HG):​n.1038-3488T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,036 control chromosomes in the GnomAD database, including 13,063 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 0.41 (13063 hom., cov: 33)
• Consequence: MIR9-3HG ENST00000536780.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 7 publications found

Genes affected

MIR9-3HG (HGNC:27388): (MIR9-3 host gene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR9-3HG	NR_015411.2	n.285-3102T>C		intron_variant	Intron 2 of 6
MIR9-3HG	NR_133001.2	n.1038-3488T>C		intron_variant	Intron 3 of 6
MIR9-3HG	NR_133002.2	n.348-3488T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR9-3HG	ENST00000536780.6	n.1038-3488T>C		intron_variant	Intron 3 of 6	3
MIR9-3HG	ENST00000538734.7	n.38-3102T>C		intron_variant	Intron 1 of 5	2
MIR9-3HG	ENST00000546186.3	n.77-3488T>C		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61817 AN: 151916 Hom.: 13058 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.407 AC: 61851 AN: 152036 Hom.: 13063 Cov.: 33 AF XY: 0.411 AC XY: 30503 AN XY: 74290

African (AFR) AF: 0.337 AC: 13955 AN: 41460

American (AMR) AF: 0.394 AC: 6017 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1448 AN: 3468

East Asian (EAS) AF: 0.224 AC: 1153 AN: 5156

South Asian (SAS) AF: 0.498 AC: 2401 AN: 4820

European-Finnish (FIN) AF: 0.451 AC: 4763 AN: 10562

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.451 AC: 30682 AN: 67976

Other (OTH) AF: 0.410 AC: 865 AN: 2110

Alfa AF: 0.438 Hom.: 25776

Bravo AF: 0.398

Asia WGS AF: 0.365 AC: 1266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.36
DANN	Benign	0.68
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs208824; hg19: chr15-89927560;