9-21504204-A-G

Variant names:

• chr9-21504204-A-G
• rs1332184
• ENST00000304425.4:n.344-26912T>C

Variant summary

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

The ENST00000304425.4(MIR31HG):​n.344-26912T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 151,996 control chromosomes in the GnomAD database, including 27,549 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 0.60 (27549 hom., cov: 31)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 9 publications found

Genes affected

MIR31HG (HGNC:37187): (MIR31 host gene) This gene produces a long non-coding RNA that acts as a host gene for miR-31. This transcript may be involved in cellular pluripotency and regulate the differentiation of myoblasts and other tissues. This RNA was found to interact with Polycomb repressive proteins to repression transcription of genes involves in cell senescence. [provided by RefSeq, Dec 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000304425.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR31HG	NR_027054.2		n.311-26912T>C		intron	N/A
	MIR31HG	NR_152877.1		n.52-26912T>C		intron	N/A
	MIR31HG	NR_152878.1		n.52-26912T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR31HG	ENST00000304425.4	TSL:2	n.344-26912T>C		intron	N/A
	MIR31HG	ENST00000654736.2		n.134-26912T>C		intron	N/A
	MIR31HG	ENST00000663833.2		n.123-26912T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91281 AN: 151878 Hom.: 27533 Cov.: 31

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.601 AC: 91330 AN: 151996 Hom.: 27549 Cov.: 31 AF XY: 0.600 AC XY: 44586 AN XY: 74312

African (AFR) AF: 0.610 AC: 25307 AN: 41470

American (AMR) AF: 0.596 AC: 9098 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2173 AN: 3472

East Asian (EAS) AF: 0.736 AC: 3804 AN: 5168

South Asian (SAS) AF: 0.528 AC: 2547 AN: 4822

European-Finnish (FIN) AF: 0.580 AC: 6122 AN: 10550

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40061 AN: 67932

Other (OTH) AF: 0.628 AC: 1326 AN: 2110

Alfa AF: 0.595 Hom.: 94779

Bravo AF: 0.606

Asia WGS AF: 0.654 AC: 2272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.077
DANN	Benign	0.60
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1332184; hg19: chr9-21504203;