5-88489807-C-T

Variant names:

• chr5-88489807-C-T
• rs17478824
• ENST00000504034.3:n.727+8866G>A

Variant summary

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

The ENST00000504034.3(MIR9-2HG):​n.727+8866G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 152,234 control chromosomes in the GnomAD database, including 555 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 0.082 (555 hom., cov: 32)
• Consequence: MIR9-2HG ENST00000504034.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 1 publications found

Genes affected

MIR9-2HG (HGNC:42810): (MIR9-2 host gene) This is an evolutionarily conserved gene that produces alternatively spliced long non-coding RNAs that may be expressed predominantly in the brain and visual cortex. These transcripts may be involved in tumorigenesis, as depletion by siRNA suppressed glioma cell division. Transcripts may also bind to and regulate the activity of miR-411-5p and argonaut 2, thereby altering the expression of genes involved in tumor growth. [provided by RefSeq, Nov 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0937 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504034.3. 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
	MIR9-2HG	ENST00000504034.3	TSL:3	n.727+8866G>A		intron	N/A
	MIR9-2HG	ENST00000715786.1		n.706+8866G>A		intron	N/A
	MIR9-2HG	ENST00000787068.1		n.649+8866G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0821 AC: 12482 AN: 152116 Hom.: 555 Cov.: 32

Gnomad AFR AF: 0.0683

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0723

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0956

Gnomad OTH AF: 0.0826

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

GnomAD4 genome AF: 0.0820 AC: 12484 AN: 152234 Hom.: 555 Cov.: 32 AF XY: 0.0812 AC XY: 6045 AN XY: 74438

African (AFR) AF: 0.0681 AC: 2830 AN: 41534

American (AMR) AF: 0.0723 AC: 1106 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3470

East Asian (EAS) AF: 0.0245 AC: 127 AN: 5180

South Asian (SAS) AF: 0.0782 AC: 377 AN: 4822

European-Finnish (FIN) AF: 0.106 AC: 1126 AN: 10604

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0956 AC: 6504 AN: 68006

Other (OTH) AF: 0.0836 AC: 177 AN: 2116

Alfa AF: 0.0873 Hom.: 1172

Bravo AF: 0.0779

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.68
DANN	Benign	0.57
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs17478824; hg19: chr5-87785624;