rs10811537

chr9-21408825-T-C

Variant summary

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

The ENST00000698343.1(MIR31HG):n.1405-5357A>G 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 0.145 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 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	ENST00000698343.1	n.1405-5357A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0582

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.155

Alfa AF: 0.189 Hom.: 1084

Bravo AF: 0.137

Asia WGS AF: 0.0870 AC: 303 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.54
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

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