ENST00000698343.1:n.103-9440G>A

Variant names:

• chr9-21430132-C-T
• rs12337364
• ENST00000698343.1:n.103-9440G>A

Variant summary

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

The ENST00000698343.1(MIR31HG):​n.103-9440G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0972 in 152,154 control chromosomes in the GnomAD database, including 750 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 0.097 (750 hom., cov: 32)
• Consequence: MIR31HG ENST00000698343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98
• Publications: 2 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000698343.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR31HG	ENST00000698343.1		n.103-9440G>A		intron	N/A
	MIR31HG	ENST00000698344.1		n.497-9440G>A		intron	N/A
	MIR31HG	ENST00000698345.1		n.255-9440G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14777 AN: 152036 Hom.: 746 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0971

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.0972 AC: 14782 AN: 152154 Hom.: 750 Cov.: 32 AF XY: 0.0987 AC XY: 7341 AN XY: 74382

African (AFR) AF: 0.122 AC: 5045 AN: 41484

American (AMR) AF: 0.107 AC: 1631 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0741 AC: 257 AN: 3470

East Asian (EAS) AF: 0.114 AC: 587 AN: 5162

South Asian (SAS) AF: 0.0968 AC: 467 AN: 4826

European-Finnish (FIN) AF: 0.101 AC: 1071 AN: 10586

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0803 AC: 5460 AN: 68016

Other (OTH) AF: 0.0863 AC: 182 AN: 2110

Alfa AF: 0.0741 Hom.: 180

Bravo AF: 0.0984

Asia WGS AF: 0.132 AC: 459 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.44
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs12337364; hg19: chr9-21430131;