rs17667894

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.59
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
use as main transcriptn.91362055A>G intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MIR17HGENST00000710414.1 linkuse as main transcriptn.3512A>G non_coding_transcript_exon_variant 2/2
MIR17HGENST00000710421.1 linkuse as main transcriptn.336+12285A>G intron_variant
MIR17HGENST00000710422.1 linkuse as main transcriptn.407+11829A>G intron_variant

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17667894; hg19: chr13-92014309; API