5-88560316-A-T

Variant names:

• chr5-88560316-A-T
• rs10491452
• ENST00000502301.6:n.218-18246T>A

Variant summary

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

The ENST00000506664.8(MIR9-2HG):​n.108-18246T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0443 in 152,292 control chromosomes in the GnomAD database, including 491 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 0.044 (491 hom., cov: 31)
• Consequence: MIR9-2HG ENST00000506664.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506664.8. 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
	MIR9-2HG	NR_015436.2		n.283-18246T>A		intron	N/A
	MIR9-2HG	NR_152235.1		n.219-18246T>A		intron	N/A
	MIR9-2HG	NR_152238.1		n.216-18246T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR9-2HG	ENST00000502301.6	TSL:4	n.218-18246T>A		intron	N/A
	MIR9-2HG	ENST00000504034.3	TSL:3	n.166-18246T>A		intron	N/A
	MIR9-2HG	ENST00000506014.6	TSL:4	n.152-18246T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0442 AC: 6722 AN: 152174 Hom.: 486 Cov.: 31

Gnomad AFR AF: 0.0437

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0480

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0168

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0443 AC: 6740 AN: 152292 Hom.: 491 Cov.: 31 AF XY: 0.0483 AC XY: 3598 AN XY: 74456

African (AFR) AF: 0.0440 AC: 1831 AN: 41576

American (AMR) AF: 0.0478 AC: 731 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00461 AC: 16 AN: 3468

East Asian (EAS) AF: 0.369 AC: 1909 AN: 5178

South Asian (SAS) AF: 0.134 AC: 644 AN: 4818

European-Finnish (FIN) AF: 0.0313 AC: 332 AN: 10622

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0168 AC: 1141 AN: 68020

Other (OTH) AF: 0.0511 AC: 108 AN: 2114

Alfa AF: 0.0301 Hom.: 23

Bravo AF: 0.0453

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.44
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10491452; hg19: chr5-87856134;