9-21408517-C-T

Variant names:

• chr9-21408517-C-T
• rs10738592
• ENST00000698343.1:n.1405-5049G>A

Variant summary

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

The ENST00000698343.1(MIR31HG):​n.1405-5049G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 151,676 control chromosomes in the GnomAD database, including 19,089 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 0.50 (19089 hom., cov: 32)
• Consequence: MIR31HG ENST00000698343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 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.1405-5049G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75511 AN: 151556 Hom.: 19071 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.416

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.498 AC: 75579 AN: 151676 Hom.: 19089 Cov.: 32 AF XY: 0.501 AC XY: 37152 AN XY: 74118

African (AFR) AF: 0.544 AC: 22501 AN: 41378

American (AMR) AF: 0.498 AC: 7601 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1396 AN: 3468

East Asian (EAS) AF: 0.694 AC: 3586 AN: 5168

South Asian (SAS) AF: 0.513 AC: 2473 AN: 4818

European-Finnish (FIN) AF: 0.464 AC: 4825 AN: 10400

Middle Eastern (MID) AF: 0.421 AC: 122 AN: 290

European-Non Finnish (NFE) AF: 0.466 AC: 31665 AN: 67894

Other (OTH) AF: 0.456 AC: 959 AN: 2104

Alfa AF: 0.476 Hom.: 5478

Bravo AF: 0.501

Asia WGS AF: 0.570 AC: 1956 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.087
DANN	Benign	0.15
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs10738592; hg19: chr9-21408516; COSMIC: COSV66504909;