9-21381287-T-G

Variant names:

• chr9-21381287-T-G
• rs647167
• ENST00000698342.1:n.726-928A>C

Variant summary

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

The ENST00000698342.1(MIR31HG):​n.726-928A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,140 control chromosomes in the GnomAD database, including 1,563 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 0.14 (1563 hom., cov: 32)
• Consequence: MIR31HG ENST00000698342.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 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	ENST00000698342.1	n.726-928A>C		intron_variant	Intron 2 of 2
MIR31HG	ENST00000773559.1	n.372-1259A>C		intron_variant	Intron 1 of 4
MIR31HG	ENST00000773560.1	n.1039-928A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21043 AN: 152020 Hom.: 1557 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.0694

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.139 AC: 21079 AN: 152140 Hom.: 1563 Cov.: 32 AF XY: 0.139 AC XY: 10344 AN XY: 74372

African (AFR) AF: 0.116 AC: 4796 AN: 41504

American (AMR) AF: 0.178 AC: 2725 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3470

East Asian (EAS) AF: 0.161 AC: 831 AN: 5164

South Asian (SAS) AF: 0.0706 AC: 341 AN: 4828

European-Finnish (FIN) AF: 0.167 AC: 1769 AN: 10588

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9590 AN: 67994

Other (OTH) AF: 0.139 AC: 293 AN: 2110

Alfa AF: 0.130 Hom.: 1622

Bravo AF: 0.139

Asia WGS AF: 0.124 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.27
DANN	Benign	0.84
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs647167; hg19: chr9-21381286; COSMIC: COSV66506020;