rs1591032

Variant names:

• chr9-21423521-T-C
• rs1591032
• ENST00000698343.1:n.103-2829A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000698343.1(MIR31HG):​n.103-2829A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,102 control chromosomes in the GnomAD database, including 2,810 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 0.19 (2810 hom., cov: 32)
• Consequence: MIR31HG ENST00000698343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.22 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.103-2829A>G		intron_variant	Intron 1 of 4
MIR31HG	ENST00000698344.1	n.497-2829A>G		intron_variant	Intron 2 of 3
MIR31HG	ENST00000698345.1	n.255-2829A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28966 AN: 151984 Hom.: 2806 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.191 AC: 28979 AN: 152102 Hom.: 2810 Cov.: 32 AF XY: 0.191 AC XY: 14178 AN XY: 74370

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.163

Alfa AF: 0.196 Hom.: 2702

Bravo AF: 0.196

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.9
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1591032; hg19: chr9-21423520;