5-88567015-C-T

Variant names:

• chr5-88567015-C-T
• rs977669
• ENST00000502301.6:n.218-24945G>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.218-24945G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0426 in 152,160 control chromosomes in the GnomAD database, including 633 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 0.043 (633 hom., cov: 32)
• Consequence: MIR9-2HG ENST00000502301.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR9-2HG	NR_015436.2	n.283-24945G>A		intron_variant	Intron 3 of 4
MIR9-2HG	NR_152235.1	n.219-24945G>A		intron_variant	Intron 2 of 3
MIR9-2HG	NR_152238.1	n.216-24945G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR9-2HG	ENST00000502301.6	n.218-24945G>A		intron_variant	Intron 3 of 4	4
MIR9-2HG	ENST00000504034.3	n.166-24945G>A		intron_variant	Intron 1 of 7	3
MIR9-2HG	ENST00000506014.6	n.152-24945G>A		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes AF: 0.0426 AC: 6474 AN: 152042 Hom.: 632 Cov.: 32

Gnomad AFR AF: 0.0284

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0460

Gnomad ASJ AF: 0.00462

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0167

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0426 AC: 6475 AN: 152160 Hom.: 633 Cov.: 32 AF XY: 0.0470 AC XY: 3500 AN XY: 74402

African (AFR) AF: 0.0284 AC: 1181 AN: 41540

American (AMR) AF: 0.0458 AC: 700 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.00462 AC: 16 AN: 3464

East Asian (EAS) AF: 0.450 AC: 2315 AN: 5150

South Asian (SAS) AF: 0.138 AC: 667 AN: 4824

European-Finnish (FIN) AF: 0.0313 AC: 331 AN: 10592

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

European-Non Finnish (NFE) AF: 0.0167 AC: 1135 AN: 68006

Other (OTH) AF: 0.0484 AC: 102 AN: 2108

Alfa AF: 0.0278 Hom.: 30

Bravo AF: 0.0433

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.66
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs977669; hg19: chr5-87862833;