9-21405364-A-G

Position:

• chr9-21405364-A-G

Variant summary

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

The ENST00000698343.1(MIR31HG):​n.1405-1896T>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 0.394 in 152,042 control chromosomes in the GnomAD database, including 13,712 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 0.39 (13712 hom., cov: 32)
• Consequence: MIR31HG ENST00000698343.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 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	ENST00000698343.1	n.1405-1896T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59789 AN: 151924 Hom.: 13690 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.394 AC: 59863 AN: 152042 Hom.: 13712 Cov.: 32 AF XY: 0.395 AC XY: 29356 AN XY: 74322

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.333

Alfa AF: 0.275 Hom.: 10048

Bravo AF: 0.411

Asia WGS AF: 0.479 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.078
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10757219; hg19: chr9-21405363;