ENST00000698343.1:n.103-20898C>T

Variant names:

• chr9-21441590-G-A
• rs28383797
• ENST00000698343.1:n.103-20898C>T

Variant summary

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

The ENST00000698343.1(MIR31HG):​n.103-20898C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 4 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=-0.96).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000698343.1	n.103-20898C>T		intron_variant	Intron 1 of 4
MIR31HG	ENST00000698344.1	n.497-20898C>T		intron_variant	Intron 2 of 3
MIR31HG	ENST00000698345.1	n.255-20898C>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.0927 AC: 3849 AN: 41540

American (AMR) AF: 0.0238 AC: 364 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0493 AC: 171 AN: 3470

East Asian (EAS) AF: 0.186 AC: 962 AN: 5172

South Asian (SAS) AF: 0.181 AC: 873 AN: 4820

European-Finnish (FIN) AF: 0.0266 AC: 282 AN: 10610

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0262 AC: 1779 AN: 68026

Other (OTH) AF: 0.0440 AC: 93 AN: 2114

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
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs28383797; hg19: chr9-21441589;