rs208824

chr15-89384329-T-C

Variant summary

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

The NR_133001.1(MIR9-3HG):n.1038-3488T>C 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 0.407 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 NR_133001.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MIR9-3HG	NR_133001.1	n.1038-3488T>C		intron_variant, non_coding_transcript_variant
MIR9-3HG	NR_015411.1	n.347-3102T>C		intron_variant, non_coding_transcript_variant
MIR9-3HG	NR_133002.1	n.336-3488T>C		intron_variant, non_coding_transcript_variant
MIR9-3HG	NR_133003.1	n.262-3102T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR9-3HG	ENST00000701636.1	n.46-3488T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.410

Alfa AF: 0.442 Hom.: 20873

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs208824; hg19: chr15-89927560;