Variant 13-91350844-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6

The ENST00000581816.1(MIR17HG):n.780A>G 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 0.000499 in 534,766 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0010 ( 1 hom., cov: 33)

Exomes 𝑓: 0.00030 ( 0 hom. )

Consequence

MIR17HG
ENST00000581816.1 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.180

Variant links:

Genes affected

MIR17HG (HGNC:):

MIR17HG links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant 13-91350844-A-G is Benign according to our data. Variant chr13-91350844-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3039825.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
MIR17HG	NR_027350.1 linkuse as main transcript	n.1287A>G	non_coding_transcript_exon_variant	2/2
MIR17HG	NR_027349.1 linkuse as main transcript	n.284+618A>G	intron_variant
MIR19A	NR_029489.1 linkuse as main transcript	n.-47A>G	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
MIR17HG	ENST00000581816.1 linkuse as main transcript	n.780A>G	non_coding_transcript_exon_variant	3/3	1
MIR17HG	ENST00000582141.6 linkuse as main transcript	n.1287A>G	non_coding_transcript_exon_variant	2/2	1
MIR17HG	ENST00000400282.7 linkuse as main transcript	n.284+618A>G	intron_variant		1

Frequencies

GnomAD3 genomes

AF:

0.00101

AC:

153

AN:

152226

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00340

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000441

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.000450

AC:

113

AN:

250852

Hom.:

AF XY:

0.000317

AC XY:

AN XY:

135788

show subpopulations

Gnomad AFR exome

AF:

0.00395

Gnomad AMR exome

AF:

0.000145

Gnomad ASJ exome

AF:

0.00318

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000706

Gnomad OTH exome

AF:

0.000327

GnomAD4 exome

AF:

0.000298

AC:

114

AN:

382422

Hom.:

Cov.:

AF XY:

0.000211

AC XY:

AN XY:

217708

show subpopulations

Gnomad4 AFR exome

AF:

0.00419

Gnomad4 AMR exome

AF:

0.000138

Gnomad4 ASJ exome

AF:

0.00366

Gnomad4 EAS exome

AF:

0.000152

Gnomad4 SAS exome

AF:

0.0000150

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000729

Gnomad4 OTH exome

AF:

0.000299

GnomAD4 genome

AF:

0.00100

AC:

153

AN:

152344

Hom.:

Cov.:

AF XY:

0.000940

AC XY:

AN XY:

74498

show subpopulations

Gnomad4 AFR

AF:

0.00339

Gnomad4 AMR

AF:

0.000131

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000441

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.000854

Hom.:

Bravo

AF:

0.00118

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

Jun 29, 2022

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

-0.52

CADD

Benign

6.3

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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