9-21368928-C-T

Variant names:

• chr9-21368928-C-T
• rs641734
• ENST00000773559.1:n.584-3840G>A

Variant summary

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

The ENST00000773559.1(MIR31HG):​n.584-3840G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 166,796 control chromosomes in the GnomAD database, including 2,800 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 0.18 (2510 hom., cov: 32)
  • Exomes 𝑓: 0.19 (290 hom.)
• Consequence: MIR31HG ENST00000773559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000773559.1	n.584-3840G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26747 AN: 151914 Hom.: 2506 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.172

GnomAD4 exome AF: 0.189 AC: 2784 AN: 14764 Hom.: 290 Cov.: 0 AF XY: 0.184 AC XY: 1290 AN XY: 6996

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.250 AC: 1 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.189 AC: 2749 AN: 14576

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.186 AC: 16 AN: 86

Other (OTH) AF: 0.193 AC: 17 AN: 88

GnomAD4 genome AF: 0.176 AC: 26765 AN: 152032 Hom.: 2510 Cov.: 32 AF XY: 0.178 AC XY: 13246 AN XY: 74316

African (AFR) AF: 0.158 AC: 6548 AN: 41476

American (AMR) AF: 0.239 AC: 3652 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3468

East Asian (EAS) AF: 0.311 AC: 1610 AN: 5180

South Asian (SAS) AF: 0.113 AC: 547 AN: 4820

European-Finnish (FIN) AF: 0.191 AC: 2015 AN: 10532

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11210 AN: 67966

Other (OTH) AF: 0.176 AC: 370 AN: 2106

Alfa AF: 0.171 Hom.: 520

Bravo AF: 0.180

Asia WGS AF: 0.194 AC: 676 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.44
PhyloP100		-2.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs641734; hg19: chr9-21368927;