5-88643836-C-T

Variant names:

• chr5-88643836-C-T
• rs10514301
• ENST00000502301.6:n.217+27200G>A

Variant summary

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

The ENST00000502301.6(MIR9-2HG):​n.217+27200G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 151,722 control chromosomes in the GnomAD database, including 2,404 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 0.16 (2404 hom., cov: 32)
• Consequence: MIR9-2HG ENST00000502301.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 17 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502301.6. 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
	MIR9-2HG	NR_015436.2		n.282+27200G>A		intron	N/A
	MIR9-2HG	NR_152235.1		n.218+27200G>A		intron	N/A
	MIR9-2HG	NR_152238.1		n.215+27200G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR9-2HG	ENST00000502301.6	TSL:4	n.217+27200G>A		intron	N/A
	MIR9-2HG	ENST00000506014.6	TSL:4	n.151+27200G>A		intron	N/A
	MIR9-2HG	ENST00000506664.8	TSL:2	n.107+34512G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24550 AN: 151604 Hom.: 2403 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0666

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.162 AC: 24563 AN: 151722 Hom.: 2404 Cov.: 32 AF XY: 0.162 AC XY: 12026 AN XY: 74142

African (AFR) AF: 0.205 AC: 8509 AN: 41414

American (AMR) AF: 0.167 AC: 2537 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 532 AN: 3462

East Asian (EAS) AF: 0.487 AC: 2520 AN: 5172

South Asian (SAS) AF: 0.181 AC: 873 AN: 4816

European-Finnish (FIN) AF: 0.0666 AC: 703 AN: 10558

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8435 AN: 67766

Other (OTH) AF: 0.161 AC: 339 AN: 2102

Alfa AF: 0.136 Hom.: 208

Bravo AF: 0.173

Asia WGS AF: 0.262 AC: 907 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.63
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10514301; hg19: chr5-87939654;