rs615544

Variant names:

• chr9-21383735-C-A
• rs615544
• ENST00000698342.1:n.726-3376G>T

Variant summary

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

The ENST00000698342.1(MIR31HG):​n.726-3376G>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000698342.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR31HG	ENST00000698342.1		n.726-3376G>T		intron	N/A
	MIR31HG	ENST00000773559.1		n.372-3707G>T		intron	N/A
	MIR31HG	ENST00000773560.1		n.1039-3376G>T		intron	N/A

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

African (AFR) AF: 0.0714 AC: 2966 AN: 41526

American (AMR) AF: 0.104 AC: 1592 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3468

East Asian (EAS) AF: 0.155 AC: 803 AN: 5176

South Asian (SAS) AF: 0.0589 AC: 284 AN: 4824

European-Finnish (FIN) AF: 0.122 AC: 1289 AN: 10576

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7804 AN: 68012

Other (OTH) AF: 0.114 AC: 241 AN: 2114

Alfa AF: 0.106 Hom.: 3973

Bravo AF: 0.0992

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.70
DANN	Benign	0.45
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs615544; hg19: chr9-21383734;