rs2304608

Variant names:

• chr5-88666480-C-A
• rs2304608
• ENST00000500197.6:n.1346G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-88666480-C-A
• chr5-88666480-C-G

Variant summary

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

The ENST00000500197.6(MIR9-2HG):​n.1346G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 224,762 control chromosomes in the GnomAD database, including 5,332 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 0.21 (3909 hom., cov: 32)
  • Exomes 𝑓: 0.18 (1423 hom.)
• Consequence: MIR9-2HG ENST00000500197.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 13 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR9-2HG	NR_024383.2	n.1327G>T		non_coding_transcript_exon_variant	Exon 4 of 4
MIR9-2HG	NR_024384.2	n.1537G>T		non_coding_transcript_exon_variant	Exon 3 of 3
MIR9-2HG	NR_152232.1	n.1417G>T		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR9-2HG	ENST00000500197.6	n.1346G>T		non_coding_transcript_exon_variant	Exon 4 of 4	1
MIR9-2HG	ENST00000505030.6	n.1922G>T		non_coding_transcript_exon_variant	Exon 3 of 3	1
MIR9-2HG	ENST00000504246.6	n.2461G>T		non_coding_transcript_exon_variant	Exon 5 of 5	2

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32379 AN: 151774 Hom.: 3912 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.214

GnomAD4 exome AF: 0.180 AC: 13108 AN: 72870 Hom.: 1423 Cov.: 0 AF XY: 0.191 AC XY: 7476 AN XY: 39152

African (AFR) AF: 0.255 AC: 237 AN: 930

American (AMR) AF: 0.189 AC: 719 AN: 3812

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 215 AN: 1528

East Asian (EAS) AF: 0.478 AC: 1031 AN: 2158

South Asian (SAS) AF: 0.246 AC: 3312 AN: 13446

European-Finnish (FIN) AF: 0.110 AC: 359 AN: 3266

Middle Eastern (MID) AF: 0.150 AC: 34 AN: 226

European-Non Finnish (NFE) AF: 0.150 AC: 6597 AN: 43896

Other (OTH) AF: 0.167 AC: 604 AN: 3608

GnomAD4 genome AF: 0.213 AC: 32397 AN: 151892 Hom.: 3909 Cov.: 32 AF XY: 0.213 AC XY: 15798 AN XY: 74228

African (AFR) AF: 0.282 AC: 11690 AN: 41394

American (AMR) AF: 0.207 AC: 3156 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 603 AN: 3466

East Asian (EAS) AF: 0.494 AC: 2538 AN: 5136

South Asian (SAS) AF: 0.277 AC: 1334 AN: 4812

European-Finnish (FIN) AF: 0.107 AC: 1125 AN: 10544

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11350 AN: 67962

Other (OTH) AF: 0.212 AC: 446 AN: 2106

Alfa AF: 0.187 Hom.: 376

Bravo AF: 0.224

Asia WGS AF: 0.319 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.46
DANN	Benign	0.55
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2304608; hg19: chr5-87962298;