rs10811568

chr9-21543445-A-G

Variant summary

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

The NR_152878.1(MIR31HG):n.51+16303T>C 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 0.109 in 151,986 control chromosomes in the GnomAD database, including 1,052 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 0.11 (1052 hom., cov: 32)
• Consequence: MIR31HG NR_152878.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR31HG	NR_152878.1	n.51+16303T>C		intron_variant, non_coding_transcript_variant
MIR31HG	NR_027054.2	n.310+16044T>C		intron_variant, non_coding_transcript_variant
MIR31HG	NR_152877.1	n.51+16303T>C		intron_variant, non_coding_transcript_variant
MIR31HG	NR_152879.1	n.310+16044T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR31HG	ENST00000698343.1	n.102+16303T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16566 AN: 151868 Hom.: 1052 Cov.: 32

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.0976

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0896

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

GnomAD4 genome AF: 0.109 AC: 16576 AN: 151986 Hom.: 1052 Cov.: 32 AF XY: 0.113 AC XY: 8380 AN XY: 74302

Gnomad4 AFR AF: 0.0875

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.0976

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0900

Alfa AF: 0.103 Hom.: 1308

Bravo AF: 0.107

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.7
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10811568; hg19: chr9-21543444;