rs12337364

Positions:

• chr9-21430132-C-T

Variant summary

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

The ENST00000698343.1(MIR31HG):​n.103-9440G>A 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 0.0972 in 152,154 control chromosomes in the GnomAD database, including 750 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 0.097 (750 hom., cov: 32)
• Consequence: MIR31HG ENST00000698343.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 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.103-9440G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14777 AN: 152036 Hom.: 746 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0971

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.0972 AC: 14782 AN: 152154 Hom.: 750 Cov.: 32 AF XY: 0.0987 AC XY: 7341 AN XY: 74382

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0741

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0968

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0803

Gnomad4 OTH AF: 0.0863

Alfa AF: 0.0556 Hom.: 72

Bravo AF: 0.0984

Asia WGS AF: 0.132 AC: 459 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12337364; hg19: chr9-21430131;