chr9-21368098-T-A

Variant names:

• chr9-21368098-T-A
• rs653778
• ENST00000773559.1:n.584-3010A>T

Variant summary

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

The ENST00000773559.1(MIR31HG):​n.584-3010A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 1,512,940 control chromosomes in the GnomAD database, including 21,092 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 0.17 (2274 hom., cov: 30)
  • Exomes 𝑓: 0.16 (18818 hom.)
• Consequence: MIR31HG ENST00000773559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.67
• Publications: 5 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]

IFNA13 (HGNC:5419): (interferon alpha 13) Predicted to enable cytokine activity and type I interferon receptor binding activity. Predicted to be involved in several processes, including B cell activation; lymphocyte activation involved in immune response; and positive regulation of peptidyl-serine phosphorylation of STAT protein. Predicted to be located in extracellular region. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNA13	NM_006900.4	c.-88A>T		upstream_gene_variant		ENST00000610660.2	NP_008831.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000773559.1	n.584-3010A>T		intron_variant	Intron 3 of 4
IFNA13	ENST00000610660.2	c.-88A>T		upstream_gene_variant		6	NM_006900.4	ENSP00000480467.1
IFNA13	ENST00000449498.2	c.-91A>T		upstream_gene_variant		6		ENSP00000394494.2

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25467 AN: 151994 Hom.: 2271 Cov.: 30

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.163

GnomAD4 exome AF: 0.163 AC: 221601 AN: 1360828 Hom.: 18818 Cov.: 23 AF XY: 0.161 AC XY: 109086 AN XY: 676862

African (AFR) AF: 0.146 AC: 4326 AN: 29722

American (AMR) AF: 0.176 AC: 5646 AN: 32132

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 4041 AN: 22544

East Asian (EAS) AF: 0.305 AC: 11885 AN: 38990

South Asian (SAS) AF: 0.112 AC: 8638 AN: 77272

European-Finnish (FIN) AF: 0.182 AC: 9464 AN: 51954

Middle Eastern (MID) AF: 0.111 AC: 605 AN: 5440

European-Non Finnish (NFE) AF: 0.160 AC: 167864 AN: 1046386

Other (OTH) AF: 0.162 AC: 9132 AN: 56388

GnomAD4 genome AF: 0.168 AC: 25484 AN: 152112 Hom.: 2274 Cov.: 30 AF XY: 0.169 AC XY: 12588 AN XY: 74360

African (AFR) AF: 0.145 AC: 6025 AN: 41488

American (AMR) AF: 0.189 AC: 2897 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3470

East Asian (EAS) AF: 0.313 AC: 1619 AN: 5166

South Asian (SAS) AF: 0.114 AC: 548 AN: 4824

European-Finnish (FIN) AF: 0.191 AC: 2016 AN: 10578

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

European-Non Finnish (NFE) AF: 0.165 AC: 11217 AN: 67976

Other (OTH) AF: 0.167 AC: 352 AN: 2112

Alfa AF: 0.173 Hom.: 279

Bravo AF: 0.167

Asia WGS AF: 0.191 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.27
PhyloP100		-3.7
PromoterAI		0.0022	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs653778; hg19: chr9-21368097; COSMIC: COSV71924594; COSMIC: COSV71924594;