9-21470998-C-T

Variant names:

• chr9-21470998-C-T
• rs7861480
• ENST00000304425.4:n.604+5901G>A

Variant summary

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

The ENST00000304425.4(MIR31HG):​n.604+5901G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,968 control chromosomes in the GnomAD database, including 6,920 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 0.25 (6920 hom., cov: 32)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000304425.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR31HG	NR_027054.2		n.571+5901G>A		intron	N/A
	MIR31HG	NR_152877.1		n.312+5901G>A		intron	N/A
	MIR31HG	NR_152878.1		n.175+6171G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR31HG	ENST00000304425.4	TSL:2	n.604+5901G>A		intron	N/A
	MIR31HG	ENST00000654736.2		n.394+5901G>A		intron	N/A
	MIR31HG	ENST00000663833.2		n.246+6171G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37237 AN: 151850 Hom.: 6890 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.246 AC: 37322 AN: 151968 Hom.: 6920 Cov.: 32 AF XY: 0.248 AC XY: 18381 AN XY: 74264

African (AFR) AF: 0.509 AC: 21076 AN: 41402

American (AMR) AF: 0.218 AC: 3323 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3470

East Asian (EAS) AF: 0.259 AC: 1334 AN: 5144

South Asian (SAS) AF: 0.304 AC: 1467 AN: 4818

European-Finnish (FIN) AF: 0.145 AC: 1541 AN: 10594

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7539 AN: 67958

Other (OTH) AF: 0.200 AC: 422 AN: 2108

Alfa AF: 0.160 Hom.: 8138

Bravo AF: 0.259

Asia WGS AF: 0.279 AC: 969 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.31
DANN	Benign	0.63
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs7861480; hg19: chr9-21470997;