chr9-21378326-G-A

Variant names:

• chr9-21378326-G-A
• rs10448208
• ENST00000773559.1:n.513-720C>T

Variant summary

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

The ENST00000773559.1(MIR31HG):​n.513-720C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 151,918 control chromosomes in the GnomAD database, including 4,836 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 0.22 (4836 hom., cov: 32)
• Consequence: MIR31HG ENST00000773559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773559.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR31HG	ENST00000773559.1		n.513-720C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33094 AN: 151800 Hom.: 4817 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.0827

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.218 AC: 33156 AN: 151918 Hom.: 4836 Cov.: 32 AF XY: 0.217 AC XY: 16106 AN XY: 74212

African (AFR) AF: 0.413 AC: 17098 AN: 41404

American (AMR) AF: 0.222 AC: 3393 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0980 AC: 340 AN: 3468

East Asian (EAS) AF: 0.270 AC: 1394 AN: 5158

South Asian (SAS) AF: 0.269 AC: 1296 AN: 4816

European-Finnish (FIN) AF: 0.0827 AC: 873 AN: 10560

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8263 AN: 67938

Other (OTH) AF: 0.189 AC: 399 AN: 2112

Alfa AF: 0.184 Hom.: 918

Bravo AF: 0.236

Asia WGS AF: 0.276 AC: 955 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.40
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10448208; hg19: chr9-21378325;