9-21407251-T-C

Position:

• chr9-21407251-T-C

Variant summary

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

The ENST00000698343.1(MIR31HG):​n.1405-3783A>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 0.507 in 152,092 control chromosomes in the GnomAD database, including 20,320 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 0.51 (20320 hom., cov: 32)
• Consequence: MIR31HG ENST00000698343.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69

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=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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.1405-3783A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77094 AN: 151974 Hom.: 20297 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.507 AC: 77165 AN: 152092 Hom.: 20320 Cov.: 32 AF XY: 0.508 AC XY: 37803 AN XY: 74348

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.473

Alfa AF: 0.436 Hom.: 6803

Bravo AF: 0.519

Asia WGS AF: 0.574 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.80
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1330322; hg19: chr9-21407250; COSMIC: COSV66504895;