5-88502419-G-C

Variant names:

• chr5-88502419-G-C
• rs2194025
• ENST00000504034.3:n.424-2654C>G

Variant summary

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

The ENST00000504034.3(MIR9-2HG):​n.424-2654C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,098 control chromosomes in the GnomAD database, including 2,136 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 0.15 (2136 hom., cov: 32)
• Consequence: MIR9-2HG ENST00000504034.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.988
• 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=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 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

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
	MIR9-2HG	ENST00000504034.3	TSL:3	n.424-2654C>G		intron	N/A
	MIR9-2HG	ENST00000715786.1		n.403-2654C>G		intron	N/A
	MIR9-2HG	ENST00000787068.1		n.346-2654C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22607 AN: 151980 Hom.: 2133 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0521

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0991

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.149 AC: 22626 AN: 152098 Hom.: 2136 Cov.: 32 AF XY: 0.151 AC XY: 11261 AN XY: 74386

African (AFR) AF: 0.214 AC: 8862 AN: 41458

American (AMR) AF: 0.120 AC: 1835 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0521 AC: 181 AN: 3472

East Asian (EAS) AF: 0.442 AC: 2274 AN: 5150

South Asian (SAS) AF: 0.182 AC: 875 AN: 4818

European-Finnish (FIN) AF: 0.143 AC: 1514 AN: 10592

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0991 AC: 6739 AN: 67998

Other (OTH) AF: 0.136 AC: 287 AN: 2114

Alfa AF: 0.0461 Hom.: 43

Bravo AF: 0.151

Asia WGS AF: 0.285 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	16
DANN	Benign	0.66
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs2194025; hg19: chr5-87798236;