Variant rs2302069 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000338034.9(ELAC2):c.680-36A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 1,591,530 control chromosomes in the GnomAD database, including 14,343 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 1050 hom., cov: 33)

Exomes 𝑓: 0.13 ( 13293 hom. )

Consequence

ELAC2
ENST00000338034.9 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.35

Variant links:

Genes affected

ELAC2 (HGNC:14198): (elaC ribonuclease Z 2) The protein encoded by this gene has a C-terminal domain with tRNA 3′ processing endoribonuclease activity, which catalyzes the removal of the 3' trailer from precursor tRNAs. The protein also interacts with activated Smad family member 2 (Smad2) and its nuclear partner forkhead box H1 (also known as FAST-1), and reduced expression can suppress transforming growth factor-beta induced growth arrest. Mutations in this gene result in an increased risk of prostate cancer. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

ELAC2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 17-13010707-T-C is Benign according to our data. Variant chr17-13010707-T-C is described in ClinVar as [Benign]. Clinvar id is 1246967.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELAC2	NM_018127.7 linkuse as main transcript	c.680-36A>G		intron_variant		ENST00000338034.9	NP_060597.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELAC2	ENST00000338034.9 linkuse as main transcript	c.680-36A>G		intron_variant		1	NM_018127.7	ENSP00000337445	P2	Q9BQ52-1

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15705

AN:

152124

Hom.:

1049

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0256

Gnomad AMI

AF:

0.0965

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.0237

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.185

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.137

Gnomad OTH

AF:

0.0941

GnomAD3 exomes

AF:

0.126

AC:

31498

AN:

249866

Hom.:

2307

AF XY:

0.127

AC XY:

17205

AN XY:

135364

show subpopulations

Gnomad AFR exome

AF:

0.0217

Gnomad AMR exome

AF:

0.157

Gnomad ASJ exome

AF:

0.115

Gnomad EAS exome

AF:

0.0273

Gnomad SAS exome

AF:

0.125

Gnomad FIN exome

AF:

0.194

Gnomad NFE exome

AF:

0.135

Gnomad OTH exome

AF:

0.137

GnomAD4 exome

AF:

0.132

AC:

190239

AN:

1439288

Hom.:

13293

Cov.:

AF XY:

0.132

AC XY:

94476

AN XY:

717786

show subpopulations

Gnomad4 AFR exome

AF:

0.0198

Gnomad4 AMR exome

AF:

0.155

Gnomad4 ASJ exome

AF:

0.111

Gnomad4 EAS exome

AF:

0.0272

Gnomad4 SAS exome

AF:

0.127

Gnomad4 FIN exome

AF:

0.187

Gnomad4 NFE exome

AF:

0.138

Gnomad4 OTH exome

AF:

0.119

GnomAD4 genome

AF:

0.103

AC:

15702

AN:

152242

Hom.:

1050

Cov.:

AF XY:

0.106

AC XY:

7866

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.0255

Gnomad4 AMR

AF:

0.128

Gnomad4 ASJ

AF:

0.115

Gnomad4 EAS

AF:

0.0236

Gnomad4 SAS

AF:

0.130

Gnomad4 FIN

AF:

0.185

Gnomad4 NFE

AF:

0.137

Gnomad4 OTH

AF:

0.0926

Alfa

AF:

0.126

Hom.:

787

Bravo

AF:

0.0930

Asia WGS

AF:

0.0650

AC:

227

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 23, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.11

DANN

Benign

0.62

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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