Variant 13-91350247-C-CT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6

The ENST00000581816.1(MIR17HG):n.186dupT 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 0.00172 in 208,504 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0019 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0014 ( 0 hom. )

Consequence

MIR17HG
ENST00000581816.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.90

Variant links:

Genes affected

MIR17HG (HGNC:):

MIR17HG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP6

Variant 13-91350247-C-CT is Benign according to our data. Variant chr13-91350247-C-CT is described in ClinVar as [Likely_benign]. Clinvar id is 3045929.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR17HG	NR_027350.1 linkuse as main transcript	n.693dupT		non_coding_transcript_exon_variant	2/2
MIR17HG	NR_027349.1 linkuse as main transcript	n.284+24dupT		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
MIR17HG	ENST00000581816.1 linkuse as main transcript	n.186dupT	non_coding_transcript_exon_variant	3/3	1
MIR17HG	ENST00000582141.6 linkuse as main transcript	n.693dupT	non_coding_transcript_exon_variant	2/2	1
MIR17HG	ENST00000400282.7 linkuse as main transcript	n.284+24dupT	intron_variant		1

Frequencies

GnomAD3 genomes

AF:

0.00187

AC:

284

AN:

152138

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000603

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00151

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00343

Gnomad OTH

AF:

0.000478

GnomAD4 exome

AF:

0.00135

AC:

AN:

56248

Hom.:

Cov.:

AF XY:

0.00115

AC XY:

AN XY:

29476

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000552

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.000298

Gnomad4 NFE exome

AF:

0.00220

Gnomad4 OTH exome

AF:

0.000659

GnomAD4 genome

AF:

0.00186

AC:

283

AN:

152256

Hom.:

Cov.:

AF XY:

0.00150

AC XY:

112

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.000602

Gnomad4 AMR

AF:

0.00144

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00343

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.00130

Hom.:

Bravo

AF:

0.00171

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

MIR17HG-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 31, 2021

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over