rs2104880

Variant names:

• chr9-21419724-C-T
• rs2104880
• ENST00000669680.1:n.3237G>A

Variant summary

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

The ENST00000669680.1(MIR31HG):​n.3237G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0747 in 152,146 control chromosomes in the GnomAD database, including 581 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 0.075 (581 hom., cov: 32)
• Consequence: MIR31HG ENST00000669680.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000669680.1	n.3237G>A		non_coding_transcript_exon_variant	Exon 1 of 3
MIR31HG	ENST00000698344.1	n.1465G>A		non_coding_transcript_exon_variant	Exon 3 of 4
MIR31HG	ENST00000698345.1	n.1223G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0746 AC: 11334 AN: 152028 Hom.: 577 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0129

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0560

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0747 AC: 11370 AN: 152146 Hom.: 581 Cov.: 32 AF XY: 0.0713 AC XY: 5300 AN XY: 74378

African (AFR) AF: 0.143 AC: 5945 AN: 41472

American (AMR) AF: 0.0570 AC: 871 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 199 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0133 AC: 64 AN: 4818

European-Finnish (FIN) AF: 0.0262 AC: 278 AN: 10596

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.0561 AC: 3814 AN: 68008

Other (OTH) AF: 0.0701 AC: 148 AN: 2112

Alfa AF: 0.0651 Hom.: 642

Bravo AF: 0.0805

Asia WGS AF: 0.0180 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.25
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2104880; hg19: chr9-21419723;