rs17667894

Positions:

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

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000710422.1(MIR17HG):​n.407+11829A>G variant causes a intron, non coding transcript 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 ENST00000710422.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.59

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR17HG	ENST00000710422.1	n.407+11829A>G		intron_variant, non_coding_transcript_variant
MIR17HG	ENST00000710414.1	n.3512A>G		non_coding_transcript_exon_variant	2/2
MIR17HG	ENST00000710421.1	n.336+12285A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0198

Gnomad4 AMR AF: 0.0307

Gnomad4 ASJ AF: 0.0596

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.0659

Gnomad4 FIN AF: 0.0530

Gnomad4 NFE AF: 0.0352

Gnomad4 OTH AF: 0.0425

Alfa AF: 0.0352 Hom.: 22

Bravo AF: 0.0397

Asia WGS AF: 0.180 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17667894; hg19: chr13-92014309;