Variant chr3-128879626-CGT-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_014049.5(ACAD9):c.-57_-56del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 1,585,160 control chromosomes in the GnomAD database, including 83,489 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.39 ( 13536 hom., cov: 0)

Exomes 𝑓: 0.30 ( 69953 hom. )

Consequence

ACAD9
NM_014049.5 5_prime_UTR

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 0.290

Variant links:

Genes affected

ACAD9 (HGNC:21497): (acyl-CoA dehydrogenase family member 9) This gene encodes a member of the acyl-CoA dehydrogenase family. Members of this family of proteins localize to the mitochondria and catalyze the rate-limiting step in the beta-oxidation of fatty acyl-CoA. The encoded protein is specifically active toward palmitoyl-CoA and long-chain unsaturated substrates. Mutations in this gene cause acyl-CoA dehydrogenase family member type 9 deficiency. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Mar 2010]

ACAD9 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 3-128879626-CGT-C is Benign according to our data. Variant chr3-128879626-CGT-C is described in ClinVar as [Benign]. Clinvar id is 343189.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
ACAD9	NM_014049.5 linkuse as main transcript	c.-57_-56del	5_prime_UTR_variant	1/18	ENST00000308982.12
ACAD9	NM_001410805.1 linkuse as main transcript	c.-332_-331del	5_prime_UTR_variant	1/17
ACAD9	NR_033426.2 linkuse as main transcript	n.16_17del	non_coding_transcript_exon_variant	1/18
ACAD9	XR_427367.4 linkuse as main transcript	n.16_17del	non_coding_transcript_exon_variant	1/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACAD9	ENST00000308982.12 linkuse as main transcript	c.-57_-56del		5_prime_UTR_variant	1/18	1	NM_014049.5	P1

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

59660

AN:

151738

Hom.:

13513

Cov.:

show subpopulations

Gnomad AFR

AF:

0.620

Gnomad AMI

AF:

0.208

Gnomad AMR

AF:

0.379

Gnomad ASJ

AF:

0.386

Gnomad EAS

AF:

0.553

Gnomad SAS

AF:

0.270

Gnomad FIN

AF:

0.236

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.283

Gnomad OTH

AF:

0.396

GnomAD3 exomes

AF:

0.333

AC:

82499

AN:

247442

Hom.:

15389

AF XY:

0.326

AC XY:

43880

AN XY:

134788

show subpopulations

Gnomad AFR exome

AF:

0.626

Gnomad AMR exome

AF:

0.330

Gnomad ASJ exome

AF:

0.390

Gnomad EAS exome

AF:

0.581

Gnomad SAS exome

AF:

0.265

Gnomad FIN exome

AF:

0.244

Gnomad NFE exome

AF:

0.286

Gnomad OTH exome

AF:

0.319

GnomAD4 exome

AF:

0.303

AC:

434806

AN:

1433306

Hom.:

69953

AF XY:

0.302

AC XY:

215648

AN XY:

714612

show subpopulations

Gnomad4 AFR exome

AF:

0.634

Gnomad4 AMR exome

AF:

0.333

Gnomad4 ASJ exome

AF:

0.394

Gnomad4 EAS exome

AF:

0.566

Gnomad4 SAS exome

AF:

0.268

Gnomad4 FIN exome

AF:

0.243

Gnomad4 NFE exome

AF:

0.285

Gnomad4 OTH exome

AF:

0.327

GnomAD4 genome

AF:

0.393

AC:

59733

AN:

151854

Hom.:

13536

Cov.:

AF XY:

0.388

AC XY:

28789

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.620

Gnomad4 AMR

AF:

0.379

Gnomad4 ASJ

AF:

0.386

Gnomad4 EAS

AF:

0.553

Gnomad4 SAS

AF:

0.270

Gnomad4 FIN

AF:

0.236

Gnomad4 NFE

AF:

0.283

Gnomad4 OTH

AF:

0.396

Alfa

AF:

0.233

Hom.:

778

Bravo

AF:

0.417

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Acyl-CoA dehydrogenase 9 deficiency

Benign:3

Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 14, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 14, 2016	- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2018

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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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