rs10811537

Variant names:

• chr9-21408825-T-C
• rs10811537
• ENST00000698343.1:n.1405-5357A>G

Variant summary

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

The ENST00000698343.1(MIR31HG):​n.1405-5357A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,114 control chromosomes in the GnomAD database, including 1,971 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 0.15 (1971 hom., cov: 32)
• Consequence: MIR31HG ENST00000698343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000698343.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR31HG	ENST00000698343.1		n.1405-5357A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22097 AN: 151996 Hom.: 1970 Cov.: 32

Gnomad AFR AF: 0.0581

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.145 AC: 22103 AN: 152114 Hom.: 1971 Cov.: 32 AF XY: 0.144 AC XY: 10714 AN XY: 74380

African (AFR) AF: 0.0582 AC: 2417 AN: 41526

American (AMR) AF: 0.133 AC: 2032 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5186

South Asian (SAS) AF: 0.150 AC: 726 AN: 4826

European-Finnish (FIN) AF: 0.178 AC: 1872 AN: 10546

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13746 AN: 67976

Other (OTH) AF: 0.155 AC: 328 AN: 2110

Alfa AF: 0.188 Hom.: 1217

Bravo AF: 0.137

Asia WGS AF: 0.0870 AC: 303 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.36
PhyloP100		-1.7
PromoterAI		-0.0093	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10811537; hg19: chr9-21408824; COSMIC: COSV66504920;