chr9-21519905-C-A

Variant names:

• chr9-21519905-C-A
• rs720974
• ENST00000304425.4:n.343+39584G>T

Variant summary

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

The ENST00000304425.4(MIR31HG):​n.343+39584G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 151,918 control chromosomes in the GnomAD database, including 20,687 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 0.52 (20687 hom., cov: 32)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR31HG	NR_027054.2	n.310+39584G>T		intron_variant	Intron 1 of 3
MIR31HG	NR_152877.1	n.51+39843G>T		intron_variant	Intron 1 of 3
MIR31HG	NR_152878.1	n.51+39843G>T		intron_variant	Intron 1 of 2
MIR31HG	NR_152879.1	n.310+39584G>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+39584G>T		intron_variant	Intron 1 of 3	2
MIR31HG	ENST00000654736.2	n.133+39843G>T		intron_variant	Intron 1 of 3
MIR31HG	ENST00000663833.2	n.122+39843G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78641 AN: 151800 Hom.: 20680 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.518 AC: 78657 AN: 151918 Hom.: 20687 Cov.: 32 AF XY: 0.519 AC XY: 38542 AN XY: 74250

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.536

Alfa AF: 0.529 Hom.: 11098

Bravo AF: 0.523

Asia WGS AF: 0.633 AC: 2197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.9
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs720974; hg19: chr9-21519904;