ENST00000698343.1:n.103-27757C>T

Variant names:

• chr9-21448449-G-A
• rs7864960
• ENST00000698343.1:n.103-27757C>T

Variant summary

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

The ENST00000698343.1(MIR31HG):​n.103-27757C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,004 control chromosomes in the GnomAD database, including 25,523 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 0.57 (25523 hom., cov: 31)
• Consequence: MIR31HG ENST00000698343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 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

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	ENST00000698343.1		n.103-27757C>T		intron	N/A
	MIR31HG	ENST00000698344.1		n.497-27757C>T		intron	N/A
	MIR31HG	ENST00000698345.1		n.255-27757C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85881 AN: 151888 Hom.: 25472 Cov.: 31

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.566 AC: 85990 AN: 152004 Hom.: 25523 Cov.: 31 AF XY: 0.563 AC XY: 41840 AN XY: 74304

African (AFR) AF: 0.748 AC: 31003 AN: 41468

American (AMR) AF: 0.542 AC: 8286 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1699 AN: 3468

East Asian (EAS) AF: 0.434 AC: 2242 AN: 5164

South Asian (SAS) AF: 0.533 AC: 2569 AN: 4818

European-Finnish (FIN) AF: 0.473 AC: 4987 AN: 10544

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33312 AN: 67948

Other (OTH) AF: 0.575 AC: 1212 AN: 2108

Alfa AF: 0.510 Hom.: 14880

Bravo AF: 0.578

Asia WGS AF: 0.501 AC: 1742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.018
DANN	Benign	0.53
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7864960; hg19: chr9-21448448; COSMIC: COSV69450813;