rs12553575

Variant names:

• chr9-21408499-A-G
• rs12553575
• ENST00000698343.1:n.1405-5031T>C

Variant summary

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

The ENST00000698343.1(MIR31HG):​n.1405-5031T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,154 control chromosomes in the GnomAD database, including 1,033 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 0.11 (1033 hom., cov: 33)
• Consequence: MIR31HG ENST00000698343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.145 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	ENST00000698343.1	n.1405-5031T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16062 AN: 152034 Hom.: 1027 Cov.: 33

Gnomad AFR AF: 0.0487

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.106 AC: 16090 AN: 152154 Hom.: 1033 Cov.: 33 AF XY: 0.108 AC XY: 8041 AN XY: 74374

African (AFR) AF: 0.0488 AC: 2029 AN: 41562

American (AMR) AF: 0.150 AC: 2291 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3470

East Asian (EAS) AF: 0.140 AC: 724 AN: 5188

South Asian (SAS) AF: 0.0648 AC: 313 AN: 4828

European-Finnish (FIN) AF: 0.156 AC: 1643 AN: 10520

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.123 AC: 8348 AN: 67992

Other (OTH) AF: 0.0995 AC: 210 AN: 2110

Alfa AF: 0.123 Hom.: 168

Bravo AF: 0.103

Asia WGS AF: 0.107 AC: 369 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.11
DANN	Benign	0.53
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs12553575; hg19: chr9-21408498;