chr9-21408694-T-C

Variant names:

• chr9-21408694-T-C
• rs10811536
• ENST00000698343.1:n.1405-5226A>G

Variant summary

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

The ENST00000698343.1(MIR31HG):​n.1405-5226A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 151,634 control chromosomes in the GnomAD database, including 1,937 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 (1937 hom., cov: 32)
• Consequence: MIR31HG ENST00000698343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 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.1405-5226A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21615 AN: 151522 Hom.: 1937 Cov.: 32

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.143 AC: 21616 AN: 151634 Hom.: 1937 Cov.: 32 AF XY: 0.142 AC XY: 10501 AN XY: 74154

African (AFR) AF: 0.0478 AC: 1983 AN: 41478

American (AMR) AF: 0.133 AC: 2025 AN: 15234

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

East Asian (EAS) AF: 0.00173 AC: 9 AN: 5188

South Asian (SAS) AF: 0.154 AC: 739 AN: 4810

European-Finnish (FIN) AF: 0.178 AC: 1833 AN: 10286

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.202 AC: 13726 AN: 67860

Other (OTH) AF: 0.154 AC: 324 AN: 2108

Alfa AF: 0.167 Hom.: 294

Bravo AF: 0.134

Asia WGS AF: 0.0860 AC: 298 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.042
DANN	Benign	0.66
PhyloP100		-2.2
PromoterAI		0.0095	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10811536; hg19: chr9-21408693; COSMIC: COSV66504916;