rs10811536

chr9-21408694-T-C

Variant summary

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

The ENST00000698343.1(MIR31HG):n.1405-5226A>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 0.143 in 151,634 control chromosomes in the GnomAD database, including 1,937 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 0.14 (1937 hom., cov: 32)
• Consequence: MIR31HG ENST00000698343.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

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.1405-5226A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21615 AN: 151522 Hom.: 1937 Cov.: 32

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.143 AC: 21616 AN: 151634 Hom.: 1937 Cov.: 32 AF XY: 0.142 AC XY: 10501 AN XY: 74154

Gnomad4 AFR AF: 0.0478

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.154

Alfa AF: 0.171 Hom.: 291

Bravo AF: 0.134

Asia WGS AF: 0.0860 AC: 298 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.042
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10811536; hg19: chr9-21408693; COSMIC: COSV66504916;