ENST00000773559.1:n.584-4228G>C

Variant names:

• chr9-21369316-C-G
• rs637949
• ENST00000773559.1:n.584-4228G>C

Variant summary

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

The ENST00000773559.1(MIR31HG):​n.584-4228G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,058 control chromosomes in the GnomAD database, including 2,440 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 0.17 (2440 hom., cov: 32)
• Consequence: MIR31HG ENST00000773559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77
• Publications: 7 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773559.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR31HG	ENST00000773559.1		n.584-4228G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26258 AN: 151940 Hom.: 2436 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.173 AC: 26278 AN: 152058 Hom.: 2440 Cov.: 32 AF XY: 0.175 AC XY: 13022 AN XY: 74314

African (AFR) AF: 0.147 AC: 6084 AN: 41484

American (AMR) AF: 0.238 AC: 3642 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 650 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1609 AN: 5170

South Asian (SAS) AF: 0.113 AC: 543 AN: 4812

European-Finnish (FIN) AF: 0.191 AC: 2016 AN: 10570

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11207 AN: 67962

Other (OTH) AF: 0.174 AC: 366 AN: 2104

Alfa AF: 0.106 Hom.: 167

Bravo AF: 0.176

Asia WGS AF: 0.193 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.14
DANN	Benign	0.38
PhyloP100		-2.8
PromoterAI		-0.00050	Neutral

Splicing

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

Other links and lift over

dbSNP: rs637949; hg19: chr9-21369315;