9-21438685-A-G

Variant names:

• chr9-21438685-A-G
• rs1332190
• ENST00000698343.1:n.103-17993T>C

Variant summary

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

The ENST00000698343.1(MIR31HG):​n.103-17993T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,014 control chromosomes in the GnomAD database, including 12,004 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 0.38 (12004 hom., cov: 32)
• Consequence: MIR31HG ENST00000698343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 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.103-17993T>C		intron_variant	Intron 1 of 4
MIR31HG	ENST00000698344.1	n.497-17993T>C		intron_variant	Intron 2 of 3
MIR31HG	ENST00000698345.1	n.255-17993T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57561 AN: 151896 Hom.: 11968 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.379 AC: 57643 AN: 152014 Hom.: 12004 Cov.: 32 AF XY: 0.375 AC XY: 27905 AN XY: 74320

African (AFR) AF: 0.559 AC: 23153 AN: 41438

American (AMR) AF: 0.352 AC: 5375 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1141 AN: 3466

East Asian (EAS) AF: 0.323 AC: 1670 AN: 5164

South Asian (SAS) AF: 0.398 AC: 1916 AN: 4814

European-Finnish (FIN) AF: 0.263 AC: 2781 AN: 10584

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20407 AN: 67950

Other (OTH) AF: 0.350 AC: 738 AN: 2106

Alfa AF: 0.340 Hom.: 23521

Bravo AF: 0.393

Asia WGS AF: 0.377 AC: 1311 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	7.6
DANN	Benign	0.83
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1332190; hg19: chr9-21438684;