rs615544

chr9-21383735-C-A

Variant summary

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

The ENST00000698342.1(MIR31HG):n.726-3376G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,194 control chromosomes in the GnomAD database, including 870 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 0.10 (870 hom., cov: 32)
• Consequence: MIR31HG ENST00000698342.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR31HG	ENST00000698342.1	n.726-3376G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15623 AN: 152076 Hom.: 868 Cov.: 32

Gnomad AFR AF: 0.0715

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.0576

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.103 AC: 15640 AN: 152194 Hom.: 870 Cov.: 32 AF XY: 0.103 AC XY: 7669 AN XY: 74392

Gnomad4 AFR AF: 0.0714

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.0589

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.114

Alfa AF: 0.108 Hom.: 1878

Bravo AF: 0.0992

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.70
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs615544; hg19: chr9-21383734;