rs17671352

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1

This summary comes from the ClinGen Evidence Repository: The c.1605+6T>C variant in ACADVL is an intronic variant which occurs in intron 16. The highest population minor allele frequency in gnomAD v2.1.1 is 0.66 in European Finnish population, which is higher than the ClinGen ACADVL Variant Curation Expert Panel threshold (≥0.007) for BA1, and therefore meets this criterion (BA1). The results from in silico splicing predictors (SpliceAI) support that this variant does not affect splicing (BP4). In summary, this variant meets the criteria to be classified as benign for autosomal recessive very long chain acyl-CoA dehydrogenase (VLCAD) deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen ACADVL Variant Curation ExpertPanel: BA1, BP4. LINK:https://erepo.genome.network/evrepo/ui/classification/CA274404/MONDO:0008723/021

Frequency

Genomes: 𝑓 0.57 ( 25315 hom., cov: 31)
Exomes 𝑓: 0.62 ( 279411 hom. )

Consequence

ACADVL
NM_000018.4 splice_region, intron

Scores

2
Splicing: ADA: 0.007159
2

Clinical Significance

Benign reviewed by expert panel B:15

Conservation

PhyloP100: -0.253
Variant links:
Genes affected
ACADVL (HGNC:92): (acyl-CoA dehydrogenase very long chain) The protein encoded by this gene is targeted to the inner mitochondrial membrane where it catalyzes the first step of the mitochondrial fatty acid beta-oxidation pathway. This acyl-Coenzyme A dehydrogenase is specific to long-chain and very-long-chain fatty acids. A deficiency in this gene product reduces myocardial fatty acid beta-oxidation and is associated with cardiomyopathy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
For more information check the summary or visit ClinGen Evidence Repository.
BA1
For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ACADVLNM_000018.4 linkc.1605+6T>C splice_region_variant, intron_variant Intron 16 of 19 ENST00000356839.10 NP_000009.1 P49748-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ACADVLENST00000356839.10 linkc.1605+6T>C splice_region_variant, intron_variant Intron 16 of 19 1 NM_000018.4 ENSP00000349297.5 P49748-1

Frequencies

GnomAD3 genomes
AF:
0.569
AC:
86437
AN:
151808
Hom.:
25290
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.434
Gnomad AMI
AF:
0.629
Gnomad AMR
AF:
0.556
Gnomad ASJ
AF:
0.586
Gnomad EAS
AF:
0.485
Gnomad SAS
AF:
0.645
Gnomad FIN
AF:
0.675
Gnomad MID
AF:
0.725
Gnomad NFE
AF:
0.636
Gnomad OTH
AF:
0.603
GnomAD3 exomes
AF:
0.598
AC:
149132
AN:
249274
Hom.:
45629
AF XY:
0.610
AC XY:
82392
AN XY:
135080
show subpopulations
Gnomad AFR exome
AF:
0.429
Gnomad AMR exome
AF:
0.492
Gnomad ASJ exome
AF:
0.592
Gnomad EAS exome
AF:
0.483
Gnomad SAS exome
AF:
0.662
Gnomad FIN exome
AF:
0.666
Gnomad NFE exome
AF:
0.643
Gnomad OTH exome
AF:
0.613
GnomAD4 exome
AF:
0.616
AC:
899884
AN:
1461136
Hom.:
279411
Cov.:
71
AF XY:
0.620
AC XY:
450287
AN XY:
726846
show subpopulations
Gnomad4 AFR exome
AF:
0.428
Gnomad4 AMR exome
AF:
0.500
Gnomad4 ASJ exome
AF:
0.598
Gnomad4 EAS exome
AF:
0.459
Gnomad4 SAS exome
AF:
0.659
Gnomad4 FIN exome
AF:
0.659
Gnomad4 NFE exome
AF:
0.627
Gnomad4 OTH exome
AF:
0.601
GnomAD4 genome
AF:
0.569
AC:
86505
AN:
151926
Hom.:
25315
Cov.:
31
AF XY:
0.572
AC XY:
42513
AN XY:
74260
show subpopulations
Gnomad4 AFR
AF:
0.434
Gnomad4 AMR
AF:
0.557
Gnomad4 ASJ
AF:
0.586
Gnomad4 EAS
AF:
0.485
Gnomad4 SAS
AF:
0.647
Gnomad4 FIN
AF:
0.675
Gnomad4 NFE
AF:
0.636
Gnomad4 OTH
AF:
0.608
Alfa
AF:
0.612
Hom.:
9258
Bravo
AF:
0.551
Asia WGS
AF:
0.578
AC:
2011
AN:
3476
EpiCase
AF:
0.654
EpiControl
AF:
0.655

ClinVar

Significance: Benign
Submissions summary: Benign:15
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

Very long chain acyl-CoA dehydrogenase deficiency Benign:8
Jan 13, 2015
Counsyl
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: literature only

- -

Nov 01, 2019
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The NM_000018.3:c.1605+6T>C (NP_000009.1:p.?) [GRCH38: NC_000017.11:g.7224399T>C] variant in ACADVL gene is interpretated to be Benign based on ACMG guidelines (PMID: 25741868). This variant has been reported. This variant meets the following evidence codes reported in the ACMG guidelines: BS1, BS2 -

Jan 13, 2018
Illumina Laboratory Services, Illumina
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Feb 23, 2022
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jul 08, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Sep 16, 2020
Natera, Inc.
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Feb 04, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jun 27, 2023
ClinGen ACADVL Variant Curation Expert Panel, ClinGen
Significance: Benign
Review Status: reviewed by expert panel
Collection Method: curation

The c.1605+6T>C variant in ACADVL is an intronic variant which occurs in intron 16. The highest population minor allele frequency in gnomAD v2.1.1 is 0.66 in European Finnish population, which is higher than the ClinGen ACADVL Variant Curation Expert Panel threshold (>=0.007) for BA1, and therefore meets this criterion (BA1). The results from in silico splicing predictors (SpliceAI) support that this variant does not affect splicing (BP4). In summary, this variant meets the criteria to be classified as benign for autosomal recessive very long chain acyl-CoA dehydrogenase (VLCAD) deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen ACADVL Variant Curation ExpertPanel: BA1, BP4. -

not specified Benign:6
Jul 25, 2013
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

-
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

-
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Aug 31, 2018
Eurofins Ntd Llc (ga)
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jul 17, 2020
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1605+6T>C variant in ACADVL is classified as benign because it has been identified in 59% (167006/280516) of the total chromosomes by gnomAD (http://gnomad.broadinstitute.org). ACMG/AMP Criteria applied: BA1. -

not provided Benign:1
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.0
DANN
Benign
0.59

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.0072
dbscSNV1_RF
Benign
0.062
SpliceAI score (max)
0.040
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.

Other links and lift over

dbSNP: rs17671352; hg19: chr17-7127718; COSMIC: COSV50040336; COSMIC: COSV50040336; API