9-21405364-A-G

Variant names:

• chr9-21405364-A-G
• rs10757219
• ENST00000698343.1:n.1405-1896T>C

Variant summary

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

The ENST00000698343.1(MIR31HG):​n.1405-1896T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,042 control chromosomes in the GnomAD database, including 13,712 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 (13712 hom., cov: 32)
• Consequence: MIR31HG ENST00000698343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 8 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 = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000698343.1	n.1405-1896T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59789 AN: 151924 Hom.: 13690 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.394 AC: 59863 AN: 152042 Hom.: 13712 Cov.: 32 AF XY: 0.395 AC XY: 29356 AN XY: 74322

African (AFR) AF: 0.617 AC: 25603 AN: 41474

American (AMR) AF: 0.390 AC: 5947 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 826 AN: 3468

East Asian (EAS) AF: 0.646 AC: 3334 AN: 5162

South Asian (SAS) AF: 0.362 AC: 1745 AN: 4820

European-Finnish (FIN) AF: 0.292 AC: 3090 AN: 10578

Middle Eastern (MID) AF: 0.301 AC: 88 AN: 292

European-Non Finnish (NFE) AF: 0.270 AC: 18348 AN: 67966

Other (OTH) AF: 0.333 AC: 704 AN: 2112

Alfa AF: 0.301 Hom.: 29839

Bravo AF: 0.411

Asia WGS AF: 0.479 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.078
DANN	Benign	0.45
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10757219; hg19: chr9-21405363;