9-21471727-C-T

Variant names:

• chr9-21471727-C-T
• rs2383192
• ENST00000304425.4:n.604+5172G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000304425.4(MIR31HG):​n.604+5172G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,050 control chromosomes in the GnomAD database, including 18,175 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 0.48 (18175 hom., cov: 33)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR31HG	NR_027054.2	n.571+5172G>A		intron_variant	Intron 3 of 3
MIR31HG	NR_152877.1	n.312+5172G>A		intron_variant	Intron 3 of 3
MIR31HG	NR_152878.1	n.175+5442G>A		intron_variant	Intron 2 of 2
MIR31HG	NR_152879.1	n.434+5442G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000304425.4	n.604+5172G>A		intron_variant	Intron 3 of 3	2
MIR31HG	ENST00000654736.2	n.394+5172G>A		intron_variant	Intron 3 of 3
MIR31HG	ENST00000663833.2	n.246+5442G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73482 AN: 151932 Hom.: 18169 Cov.: 33

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.483 AC: 73499 AN: 152050 Hom.: 18175 Cov.: 33 AF XY: 0.484 AC XY: 35954 AN XY: 74320

African (AFR) AF: 0.389 AC: 16141 AN: 41482

American (AMR) AF: 0.495 AC: 7552 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1801 AN: 3470

East Asian (EAS) AF: 0.707 AC: 3659 AN: 5174

South Asian (SAS) AF: 0.471 AC: 2275 AN: 4826

European-Finnish (FIN) AF: 0.476 AC: 5023 AN: 10554

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35273 AN: 67960

Other (OTH) AF: 0.522 AC: 1103 AN: 2112

Alfa AF: 0.518 Hom.: 80810

Bravo AF: 0.490

Asia WGS AF: 0.599 AC: 2082 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.17
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2383192; hg19: chr9-21471726;