chr9-21543445-A-G

Variant names:

• chr9-21543445-A-G
• rs10811568
• ENST00000304425.4:n.343+16044T>C

Variant summary

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

The ENST00000304425.4(MIR31HG):​n.343+16044T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 151,986 control chromosomes in the GnomAD database, including 1,052 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 0.11 (1052 hom., cov: 32)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 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.310+16044T>C		intron	N/A
	MIR31HG	NR_152877.1		n.51+16303T>C		intron	N/A
	MIR31HG	NR_152878.1		n.51+16303T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR31HG	ENST00000304425.4	TSL:2	n.343+16044T>C		intron	N/A
	MIR31HG	ENST00000654736.2		n.133+16303T>C		intron	N/A
	MIR31HG	ENST00000663833.2		n.122+16303T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16566 AN: 151868 Hom.: 1052 Cov.: 32

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.0976

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0896

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

GnomAD4 genome AF: 0.109 AC: 16576 AN: 151986 Hom.: 1052 Cov.: 32 AF XY: 0.113 AC XY: 8380 AN XY: 74302

African (AFR) AF: 0.0875 AC: 3632 AN: 41500

American (AMR) AF: 0.124 AC: 1899 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1242 AN: 5134

South Asian (SAS) AF: 0.261 AC: 1258 AN: 4814

European-Finnish (FIN) AF: 0.0976 AC: 1036 AN: 10612

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6870 AN: 67880

Other (OTH) AF: 0.0900 AC: 190 AN: 2110

Alfa AF: 0.103 Hom.: 1986

Bravo AF: 0.107

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.38
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs10811568; hg19: chr9-21543444;