rs28383797

chr9-21441590-G-A

Variant summary

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

The ENST00000698343.1(MIR31HG):n.103-20898C>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 0.0555 in 152,252 control chromosomes in the GnomAD database, including 389 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 0.055 (389 hom., cov: 31)
• Consequence: MIR31HG ENST00000698343.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 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.103-20898C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0554 AC: 8429 AN: 152134 Hom.: 387 Cov.: 31

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0237

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0266

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0261

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0555 AC: 8446 AN: 152252 Hom.: 389 Cov.: 31 AF XY: 0.0582 AC XY: 4336 AN XY: 74444

Gnomad4 AFR AF: 0.0927

Gnomad4 AMR AF: 0.0238

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.0266

Gnomad4 NFE AF: 0.0262

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0412 Hom.: 18

Bravo AF: 0.0551

Asia WGS AF: 0.150 AC: 520 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.2
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28383797; hg19: chr9-21441589;