chr9-21428771-T-C

Variant names:

• chr9-21428771-T-C
• rs7043990
• ENST00000698343.1:n.103-8079A>G

Variant summary

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

The ENST00000698343.1(MIR31HG):​n.103-8079A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,272 control chromosomes in the GnomAD database, including 1,317 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 0.13 (1317 hom., cov: 33)
• Consequence: MIR31HG ENST00000698343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000698343.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR31HG	ENST00000698343.1		n.103-8079A>G		intron	N/A
	MIR31HG	ENST00000698344.1		n.497-8079A>G		intron	N/A
	MIR31HG	ENST00000698345.1		n.255-8079A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19688 AN: 152154 Hom.: 1315 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.129 AC: 19687 AN: 152272 Hom.: 1317 Cov.: 33 AF XY: 0.130 AC XY: 9679 AN XY: 74454

African (AFR) AF: 0.135 AC: 5619 AN: 41560

American (AMR) AF: 0.138 AC: 2116 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3472

East Asian (EAS) AF: 0.114 AC: 591 AN: 5190

South Asian (SAS) AF: 0.109 AC: 524 AN: 4824

European-Finnish (FIN) AF: 0.136 AC: 1446 AN: 10602

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8395 AN: 68014

Other (OTH) AF: 0.122 AC: 258 AN: 2112

Alfa AF: 0.129 Hom.: 1560

Bravo AF: 0.131

Asia WGS AF: 0.143 AC: 496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.53
DANN	Benign	0.62
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs7043990; hg19: chr9-21428770;