9-21467713-A-G

Variant names:

• chr9-21467713-A-G
• rs1888888
• ENST00000304425.4:n.604+9186T>C

Variant summary

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

The ENST00000304425.4(MIR31HG):​n.604+9186T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 152,326 control chromosomes in the GnomAD database, including 70,570 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 0.96 (70570 hom., cov: 32)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 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.571+9186T>C		intron	N/A
	MIR31HG	NR_152877.1		n.312+9186T>C		intron	N/A
	MIR31HG	NR_152878.1		n.175+9456T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR31HG	ENST00000304425.4	TSL:2	n.604+9186T>C		intron	N/A
	MIR31HG	ENST00000654736.2		n.394+9186T>C		intron	N/A
	MIR31HG	ENST00000663833.2		n.246+9456T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146459 AN: 152208 Hom.: 70510 Cov.: 32

Gnomad AFR AF: 0.989

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.995

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.977

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

GnomAD4 genome AF: 0.962 AC: 146578 AN: 152326 Hom.: 70570 Cov.: 32 AF XY: 0.965 AC XY: 71873 AN XY: 74502

African (AFR) AF: 0.989 AC: 41125 AN: 41582

American (AMR) AF: 0.976 AC: 14934 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.985 AC: 3421 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5190 AN: 5190

South Asian (SAS) AF: 0.995 AC: 4798 AN: 4822

European-Finnish (FIN) AF: 0.955 AC: 10138 AN: 10614

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.936 AC: 63712 AN: 68032

Other (OTH) AF: 0.977 AC: 2065 AN: 2114

Alfa AF: 0.944 Hom.: 8426

Bravo AF: 0.966

Asia WGS AF: 0.995 AC: 3459 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.82
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs1888888; hg19: chr9-21467712;