chr9-21408517-C-T

Position:

• chr9-21408517-C-T

Variant summary

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

The ENST00000698343.1(MIR31HG):​n.1405-5049G>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 0.498 in 151,676 control chromosomes in the GnomAD database, including 19,089 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 0.50 (19089 hom., cov: 32)
• Consequence: MIR31HG ENST00000698343.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

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 (EAS) allele frequency at 95% confidence interval = 0.675 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.1405-5049G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75511 AN: 151556 Hom.: 19071 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.416

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.498 AC: 75579 AN: 151676 Hom.: 19089 Cov.: 32 AF XY: 0.501 AC XY: 37152 AN XY: 74118

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.456

Alfa AF: 0.475 Hom.: 4936

Bravo AF: 0.501

Asia WGS AF: 0.570 AC: 1956 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.087
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10738592; hg19: chr9-21408516; COSMIC: COSV66504909;