ENST00000304425.4:n.343+28879C>T

Variant names:

• chr9-21530610-G-A
• rs10811561
• ENST00000304425.4:n.343+28879C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000304425.4(MIR31HG):​n.343+28879C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 149,430 control chromosomes in the GnomAD database, including 24,378 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 0.57 (24378 hom., cov: 31)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR31HG	NR_027054.2	n.310+28879C>T		intron_variant	Intron 1 of 3
MIR31HG	NR_152877.1	n.51+29138C>T		intron_variant	Intron 1 of 3
MIR31HG	NR_152878.1	n.51+29138C>T		intron_variant	Intron 1 of 2
MIR31HG	NR_152879.1	n.310+28879C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000304425.4	n.343+28879C>T		intron_variant	Intron 1 of 3	2
MIR31HG	ENST00000654736.2	n.133+29138C>T		intron_variant	Intron 1 of 3
MIR31HG	ENST00000663833.2	n.122+29138C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.571 AC: 85300 AN: 149314 Hom.: 24353 Cov.: 31

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.568

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.571 AC: 85362 AN: 149430 Hom.: 24378 Cov.: 31 AF XY: 0.569 AC XY: 41630 AN XY: 73104

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.589

Alfa AF: 0.557 Hom.: 46390

Bravo AF: 0.590

Asia WGS AF: 0.633 AC: 2200 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10811561; hg19: chr9-21530609;