rs7025006

Variant names:

• chr9-21415688-G-A
• rs7025006
• ENST00000669680.1:n.5162+1138C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-21415688-G-A
• chr9-21415688-G-C
• chr9-21415688-G-T

Variant summary

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

The ENST00000669680.1(MIR31HG):​n.5162+1138C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 152,034 control chromosomes in the GnomAD database, including 20,464 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 0.51 (20464 hom., cov: 32)
• Consequence: MIR31HG ENST00000669680.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98
• Publications: 9 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000669680.1. 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	ENST00000669680.1		n.5162+1138C>T		intron	N/A
	MIR31HG	ENST00000698343.1		n.1404+2218C>T		intron	N/A
	MIR31HG	ENST00000698344.1		n.3283+2218C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77508 AN: 151916 Hom.: 20432 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.510 AC: 77591 AN: 152034 Hom.: 20464 Cov.: 32 AF XY: 0.513 AC XY: 38120 AN XY: 74302

African (AFR) AF: 0.643 AC: 26670 AN: 41448

American (AMR) AF: 0.497 AC: 7590 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1332 AN: 3466

East Asian (EAS) AF: 0.563 AC: 2913 AN: 5178

South Asian (SAS) AF: 0.480 AC: 2309 AN: 4812

European-Finnish (FIN) AF: 0.485 AC: 5122 AN: 10570

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30083 AN: 67970

Other (OTH) AF: 0.482 AC: 1016 AN: 2106

Alfa AF: 0.461 Hom.: 71011

Bravo AF: 0.519

Asia WGS AF: 0.524 AC: 1825 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.035
DANN	Benign	0.25
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs7025006; hg19: chr9-21415687; COSMIC: COSV70696850;