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 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

Genes affected

MIR17HG (HGNC:):

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
		n.91362055A>G		intergenic_region

Ensembl

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