rs4978113

chr9-21401107-T-C

Variant summary

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

The ENST00000698373.1(MIR31HG):n.2439A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,164 control chromosomes in the GnomAD database, including 2,697 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 0.18 (2697 hom., cov: 32)
• Consequence: MIR31HG ENST00000698373.1 non_coding_transcript_exon
• 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=-0.49).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 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	ENST00000698373.1	n.2439A>G		non_coding_transcript_exon_variant	2/2
MIR31HG	ENST00000698342.1	n.725+1684A>G		intron_variant, non_coding_transcript_variant
MIR31HG	ENST00000698374.1	n.1118-151A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27067 AN: 152046 Hom.: 2695 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.178 AC: 27092 AN: 152164 Hom.: 2697 Cov.: 32 AF XY: 0.182 AC XY: 13567 AN XY: 74380

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.157

Alfa AF: 0.184 Hom.: 3511

Bravo AF: 0.173

Asia WGS AF: 0.247 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	15
Dann	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4978113; hg19: chr9-21401106;