rs17421627

Variant names:

• chr5-88551768-T-G
• rs17421627
• ENST00000787113.1:n.130A>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000787113.1(MIR9-2HG):​n.130A>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0495 in 152,284 control chromosomes in the GnomAD database, including 256 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 0.050 (256 hom., cov: 32)
• Consequence: MIR9-2HG ENST00000787113.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.45
• Publications: 30 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR9-2HG	NR_015436.2	n.283-9698A>C		intron_variant	Intron 3 of 4
MIR9-2HG	NR_152235.1	n.219-9698A>C		intron_variant	Intron 2 of 3
MIR9-2HG	NR_152238.1	n.216-9698A>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR9-2HG	ENST00000787113.1	n.130A>C		non_coding_transcript_exon_variant	Exon 1 of 3
MIR9-2HG	ENST00000502301.6	n.218-9698A>C		intron_variant	Intron 3 of 4	4
MIR9-2HG	ENST00000504034.3	n.166-9698A>C		intron_variant	Intron 1 of 7	3

Frequencies

GnomAD3 genomes AF: 0.0495 AC: 7539 AN: 152166 Hom.: 256 Cov.: 32

Gnomad AFR AF: 0.0132

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.0373

Gnomad FIN AF: 0.0812

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0719

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0495 AC: 7539 AN: 152284 Hom.: 256 Cov.: 32 AF XY: 0.0490 AC XY: 3647 AN XY: 74448

African (AFR) AF: 0.0132 AC: 547 AN: 41570

American (AMR) AF: 0.0474 AC: 724 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3472

East Asian (EAS) AF: 0.0151 AC: 78 AN: 5182

South Asian (SAS) AF: 0.0375 AC: 181 AN: 4822

European-Finnish (FIN) AF: 0.0812 AC: 862 AN: 10612

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0719 AC: 4889 AN: 68024

Other (OTH) AF: 0.0546 AC: 115 AN: 2108

Alfa AF: 0.0629 Hom.: 969

Bravo AF: 0.0452

Asia WGS AF: 0.0280 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	18
DANN	Benign	0.88
PhyloP100		6.4

Splicing

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

Other links and lift over

dbSNP: rs17421627; hg19: chr5-87847586;