rs594544

Variant names:

• chr9-21372124-G-A
• rs594544
• ENST00000773559.1:n.583+5412C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-21372124-G-A
• chr9-21372124-G-C
• chr9-21372124-G-T

Variant summary

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

The ENST00000773559.1(MIR31HG):​n.583+5412C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,002 control chromosomes in the GnomAD database, including 12,554 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 0.39 (12554 hom., cov: 31)
• Consequence: MIR31HG ENST00000773559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 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

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	ENST00000773559.1		n.583+5412C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58723 AN: 151884 Hom.: 12530 Cov.: 31

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.387 AC: 58799 AN: 152002 Hom.: 12554 Cov.: 31 AF XY: 0.389 AC XY: 28921 AN XY: 74258

African (AFR) AF: 0.545 AC: 22590 AN: 41434

American (AMR) AF: 0.414 AC: 6328 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3468

East Asian (EAS) AF: 0.644 AC: 3308 AN: 5136

South Asian (SAS) AF: 0.380 AC: 1828 AN: 4810

European-Finnish (FIN) AF: 0.301 AC: 3190 AN: 10582

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.288 AC: 19573 AN: 67972

Other (OTH) AF: 0.352 AC: 743 AN: 2112

Alfa AF: 0.328 Hom.: 4061

Bravo AF: 0.401

Asia WGS AF: 0.494 AC: 1719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.52
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs594544; hg19: chr9-21372123;