9-21391699-T-C

Variant names:

• chr9-21391699-T-C
• rs1224391
• ENST00000698342.1:n.725+11092A>G

Variant summary

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

The ENST00000698342.1(MIR31HG):​n.725+11092A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,042 control chromosomes in the GnomAD database, including 42,527 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 0.74 (42527 hom., cov: 31)
• Consequence: MIR31HG ENST00000698342.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 7 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.927 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.725+11092A>G		intron_variant	Intron 2 of 2
MIR31HG	ENST00000773559.1	n.371+10732A>G		intron_variant	Intron 1 of 4
MIR31HG	ENST00000773560.1	n.1038+10732A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111708 AN: 151924 Hom.: 42465 Cov.: 31

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.736 AC: 111829 AN: 152042 Hom.: 42527 Cov.: 31 AF XY: 0.735 AC XY: 54642 AN XY: 74296

African (AFR) AF: 0.935 AC: 38778 AN: 41486

American (AMR) AF: 0.717 AC: 10954 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2171 AN: 3470

East Asian (EAS) AF: 0.911 AC: 4708 AN: 5168

South Asian (SAS) AF: 0.737 AC: 3552 AN: 4820

European-Finnish (FIN) AF: 0.609 AC: 6416 AN: 10538

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42965 AN: 67962

Other (OTH) AF: 0.726 AC: 1534 AN: 2112

Alfa AF: 0.660 Hom.: 42189

Bravo AF: 0.753

Asia WGS AF: 0.836 AC: 2904 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	0.84
DANN	Benign	0.23
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1224391; hg19: chr9-21391698; COSMIC: COSV73905110;