chr17-7219921-T-TGGGCGTGCAGGACGC

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The ENST00000350303.9(ACADVL):​c.-63_-49dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 1,554,922 control chromosomes in the GnomAD database, including 250,780 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.51 ( 20943 hom., cov: 0)
Exomes 𝑓: 0.57 ( 229837 hom. )

Consequence

ACADVL
ENST00000350303.9 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.14
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 -16 ACMG points.

BP6
Variant 17-7219921-T-TGGGCGTGCAGGACGC is Benign according to our data. Variant chr17-7219921-T-TGGGCGTGCAGGACGC is described in ClinVar as [Benign]. Clinvar id is 166637.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ACADVLNM_000018.4 linkuse as main transcript upstream_gene_variant ENST00000356839.10 NP_000009.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ACADVLENST00000356839.10 linkuse as main transcript upstream_gene_variant 1 NM_000018.4 ENSP00000349297 P1P49748-1

Frequencies

GnomAD3 genomes
AF:
0.513
AC:
77778
AN:
151612
Hom.:
20921
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.338
Gnomad AMI
AF:
0.546
Gnomad AMR
AF:
0.521
Gnomad ASJ
AF:
0.559
Gnomad EAS
AF:
0.482
Gnomad SAS
AF:
0.595
Gnomad FIN
AF:
0.648
Gnomad MID
AF:
0.672
Gnomad NFE
AF:
0.589
Gnomad OTH
AF:
0.547
GnomAD4 exome
AF:
0.569
AC:
798723
AN:
1403190
Hom.:
229837
Cov.:
99
AF XY:
0.572
AC XY:
396860
AN XY:
693630
show subpopulations
Gnomad4 AFR exome
AF:
0.330
Gnomad4 AMR exome
AF:
0.476
Gnomad4 ASJ exome
AF:
0.569
Gnomad4 EAS exome
AF:
0.453
Gnomad4 SAS exome
AF:
0.605
Gnomad4 FIN exome
AF:
0.611
Gnomad4 NFE exome
AF:
0.580
Gnomad4 OTH exome
AF:
0.551
GnomAD4 genome
AF:
0.513
AC:
77841
AN:
151732
Hom.:
20943
Cov.:
0
AF XY:
0.518
AC XY:
38438
AN XY:
74168
show subpopulations
Gnomad4 AFR
AF:
0.338
Gnomad4 AMR
AF:
0.522
Gnomad4 ASJ
AF:
0.559
Gnomad4 EAS
AF:
0.481
Gnomad4 SAS
AF:
0.597
Gnomad4 FIN
AF:
0.648
Gnomad4 NFE
AF:
0.589
Gnomad4 OTH
AF:
0.551
Alfa
AF:
0.484
Hom.:
2208

ClinVar

Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Very long chain acyl-CoA dehydrogenase deficiency Benign:2
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 08, 2021- -
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Feb 03, 2014- -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 23, 2018- -

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.

Other links and lift over

dbSNP: rs6145976; hg19: chr17-7123240; API