9-21388713-G-A

Position:

• chr9-21388713-G-A

Variant summary

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

The ENST00000698342.1(MIR31HG):​n.726-8354C>T 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 0.421 in 152,018 control chromosomes in the GnomAD database, including 15,650 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 0.42 (15650 hom., cov: 32)
• Consequence: MIR31HG ENST00000698342.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000698342.1	n.726-8354C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63851 AN: 151898 Hom.: 15622 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.421 AC: 63938 AN: 152018 Hom.: 15650 Cov.: 32 AF XY: 0.422 AC XY: 31323 AN XY: 74306

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.375

Alfa AF: 0.315 Hom.: 1513

Bravo AF: 0.440

Asia WGS AF: 0.495 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs632941; hg19: chr9-21388712;