Variant chr13-91353141-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6

The ENST00000582141.6(MIR17HG):n.3584C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00041 ( 0 hom., cov: 29)

Failed GnomAD Quality Control

Consequence

MIR17HG
ENST00000582141.6 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.654

Variant links:

Genes affected

MIR17HG (HGNC:):

MIR17HG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 13-91353141-C-A is Benign according to our data. Variant chr13-91353141-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 3032970.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.3584C>A		non_coding_transcript_exon_variant	2/2
MIR17HG	NR_027349.1 linkuse as main transcript	n.285-792C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
MIR17HG	ENST00000582141.6 linkuse as main transcript	n.3584C>A	non_coding_transcript_exon_variant	2/2	1
MIR17HG	ENST00000400282.7 linkuse as main transcript	n.285-792C>A	intron_variant		1
MIR17HG	ENST00000710419.1 linkuse as main transcript	n.771C>A	non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

130888

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000366

Gnomad AMI

AF:

0.00120

Gnomad AMR

AF:

0.000474

Gnomad ASJ

AF:

0.000310

Gnomad EAS

AF:

0.00143

Gnomad SAS

AF:

0.00130

Gnomad FIN

AF:

0.000613

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000274

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000412

AC:

AN:

130924

Hom.:

Cov.:

AF XY:

0.000478

AC XY:

AN XY:

62778

show subpopulations

Gnomad4 AFR

AF:

0.000366

Gnomad4 AMR

AF:

0.000552

Gnomad4 ASJ

AF:

0.000310

Gnomad4 EAS

AF:

0.00143

Gnomad4 SAS

AF:

0.00130

Gnomad4 FIN

AF:

0.000613

Gnomad4 NFE

AF:

0.000274

Gnomad4 OTH

AF:

0.00

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

Aug 30, 2023

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

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.63

DANN

Benign

0.18

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