rs17667894

Variant names:

• chr13-91362055-A-G
• rs17667894
• ENST00000710414.1:n.3512A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-91362055-A-G
• chr13-91362055-A-T

Variant summary

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

The ENST00000710414.1(MIR17HG):​n.3512A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0407 in 152,290 control chromosomes in the GnomAD database, including 280 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 0.041 (280 hom., cov: 32)
• Consequence: MIR17HG ENST00000710414.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.59
• Publications: 5 publications found

Genes affected

MIR17HG (HGNC:23564): (miR-17-92a-1 cluster host gene) This gene is the host gene for the MIR17-92 cluster, a group of at least six microRNAs (miRNAs) that may be involved in cell survival, proliferation, differentiation, and angiogenesis. Amplification of this gene has been found in several lymphomas and solid tumors. Two non-protein coding transcript variants have been found for this host gene, but only the longest is a polycistronic transcript containing the MIR17-92 cluster. [provided by RefSeq, May 2012]

MIR17HG Gene-Disease associations (from GenCC):

• Feingold syndrome type 2

  Inheritance: AD, Unknown Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000710414.1. 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
	MIR17HG	ENST00000710414.1		n.3512A>G		non_coding_transcript_exon	Exon 2 of 2
	MIR17HG	ENST00000710421.1		n.336+12285A>G		intron	N/A
	MIR17HG	ENST00000710422.1		n.407+11829A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0407 AC: 6197 AN: 152172 Hom.: 280 Cov.: 32

Gnomad AFR AF: 0.0198

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.0596

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.0654

Gnomad FIN AF: 0.0530

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0351

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0407 AC: 6194 AN: 152290 Hom.: 280 Cov.: 32 AF XY: 0.0419 AC XY: 3123 AN XY: 74462

African (AFR) AF: 0.0198 AC: 824 AN: 41584

American (AMR) AF: 0.0307 AC: 469 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0596 AC: 207 AN: 3472

East Asian (EAS) AF: 0.238 AC: 1230 AN: 5178

South Asian (SAS) AF: 0.0659 AC: 318 AN: 4826

European-Finnish (FIN) AF: 0.0530 AC: 563 AN: 10614

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0352 AC: 2390 AN: 67994

Other (OTH) AF: 0.0425 AC: 90 AN: 2116

Alfa AF: 0.0350 Hom.: 22

Bravo AF: 0.0397

Asia WGS AF: 0.180 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	18
DANN	Benign	0.87
PhyloP100		3.6

Splicing

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

Other links and lift over

dbSNP: rs17667894; hg19: chr13-92014309;