9-21471500-C-T

Variant names:

• chr9-21471500-C-T
• rs1412395
• ENST00000304425.4:n.604+5399G>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+5399G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,014 control chromosomes in the GnomAD database, including 28,011 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 0.60 (28011 hom., cov: 32)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR31HG	NR_027054.2		n.571+5399G>A		intron	N/A
	MIR31HG	NR_152877.1		n.312+5399G>A		intron	N/A
	MIR31HG	NR_152878.1		n.175+5669G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR31HG	ENST00000304425.4	TSL:2	n.604+5399G>A		intron	N/A
	MIR31HG	ENST00000654736.2		n.394+5399G>A		intron	N/A
	MIR31HG	ENST00000663833.2		n.246+5669G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91635 AN: 151896 Hom.: 27995 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.603 AC: 91689 AN: 152014 Hom.: 28011 Cov.: 32 AF XY: 0.605 AC XY: 44975 AN XY: 74298

African (AFR) AF: 0.561 AC: 23247 AN: 41450

American (AMR) AF: 0.622 AC: 9494 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2001 AN: 3468

East Asian (EAS) AF: 0.920 AC: 4760 AN: 5172

South Asian (SAS) AF: 0.706 AC: 3407 AN: 4826

European-Finnish (FIN) AF: 0.570 AC: 6032 AN: 10576

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40711 AN: 67940

Other (OTH) AF: 0.612 AC: 1292 AN: 2110

Alfa AF: 0.603 Hom.: 14039

Bravo AF: 0.610

Asia WGS AF: 0.793 AC: 2753 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.33
DANN	Benign	0.48
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1412395; hg19: chr9-21471499;