rs7048384

Variant names:

• chr9-21461791-C-T
• rs7048384
• ENST00000304425.4:n.605-5847G>A

Variant summary

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

The ENST00000304425.4(MIR31HG):​n.605-5847G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0558 in 152,002 control chromosomes in the GnomAD database, including 511 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 0.056 (511 hom., cov: 32)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR31HG	NR_027054.2	n.572-5847G>A		intron_variant	Intron 3 of 3
MIR31HG	NR_152877.1	n.313-5847G>A		intron_variant	Intron 3 of 3
MIR31HG	NR_152878.1	n.176-5847G>A		intron_variant	Intron 2 of 2
MIR31HG	NR_152879.1	n.435-5847G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000304425.4	n.605-5847G>A		intron_variant	Intron 3 of 3	2
MIR31HG	ENST00000654736.2	n.395-5847G>A		intron_variant	Intron 3 of 3
MIR31HG	ENST00000663833.2	n.247-5847G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0558 AC: 8476 AN: 151884 Hom.: 509 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0736

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00611

Gnomad OTH AF: 0.0500

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

GnomAD4 genome AF: 0.0558 AC: 8485 AN: 152002 Hom.: 511 Cov.: 32 AF XY: 0.0594 AC XY: 4417 AN XY: 74324

African (AFR) AF: 0.117 AC: 4861 AN: 41444

American (AMR) AF: 0.0738 AC: 1128 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3464

East Asian (EAS) AF: 0.189 AC: 977 AN: 5168

South Asian (SAS) AF: 0.156 AC: 749 AN: 4814

European-Finnish (FIN) AF: 0.0184 AC: 194 AN: 10566

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00611 AC: 415 AN: 67954

Other (OTH) AF: 0.0490 AC: 103 AN: 2102

Alfa AF: 0.0352 Hom.: 37

Bravo AF: 0.0607

Asia WGS AF: 0.134 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.40
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs7048384; hg19: chr9-21461790;