ENST00000304425.4:n.343+39584G>T

Variant names:

• chr9-21519905-C-A
• rs720974
• ENST00000304425.4:n.343+39584G>T

Variant summary

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

The ENST00000304425.4(MIR31HG):​n.343+39584G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 151,918 control chromosomes in the GnomAD database, including 20,687 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 0.52 (20687 hom., cov: 32)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364
• Publications: 9 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR31HG	NR_027054.2	n.310+39584G>T		intron_variant	Intron 1 of 3
MIR31HG	NR_152877.1	n.51+39843G>T		intron_variant	Intron 1 of 3
MIR31HG	NR_152878.1	n.51+39843G>T		intron_variant	Intron 1 of 2
MIR31HG	NR_152879.1	n.310+39584G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000304425.4	n.343+39584G>T		intron_variant	Intron 1 of 3	2
MIR31HG	ENST00000654736.2	n.133+39843G>T		intron_variant	Intron 1 of 3
MIR31HG	ENST00000663833.2	n.122+39843G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78641 AN: 151800 Hom.: 20680 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.518 AC: 78657 AN: 151918 Hom.: 20687 Cov.: 32 AF XY: 0.519 AC XY: 38542 AN XY: 74250

African (AFR) AF: 0.443 AC: 18361 AN: 41448

American (AMR) AF: 0.529 AC: 8058 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1850 AN: 3468

East Asian (EAS) AF: 0.726 AC: 3743 AN: 5154

South Asian (SAS) AF: 0.513 AC: 2471 AN: 4816

European-Finnish (FIN) AF: 0.524 AC: 5529 AN: 10542

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36676 AN: 67938

Other (OTH) AF: 0.536 AC: 1132 AN: 2110

Alfa AF: 0.531 Hom.: 12381

Bravo AF: 0.523

Asia WGS AF: 0.633 AC: 2197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.9
DANN	Benign	0.74
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs720974; hg19: chr9-21519904;