dbSNP rs2286963: ACADL:p.Lys333Gln (chr2-210195326-T-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001608.4(ACADL):c.997A>C(p.Lys333Gln) variant causes a missense change. The variant allele was found at a frequency of 0.329 in 1,610,748 control chromosomes in the GnomAD database, including 90,533 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 6325 hom., cov: 32)

Exomes 𝑓: 0.33 ( 84208 hom. )

Consequence

ACADL
NM_001608.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts U:1B:2

Conservation

PhyloP100: 7.11

Publications

73 publications found

Variant links:

Genes affected

ACADL (HGNC:88): (acyl-CoA dehydrogenase long chain) The protein encoded by this gene belongs to the acyl-CoA dehydrogenase family, which is a family of mitochondrial flavoenzymes involved in fatty acid and branched chain amino-acid metabolism. This protein is one of the four enzymes that catalyze the initial step of mitochondrial beta-oxidation of straight-chain fatty acid. Defects in this gene are the cause of long-chain acyl-CoA dehydrogenase (LCAD) deficiency, leading to nonketotic hypoglycemia. [provided by RefSeq, Jul 2008]

ACADL Gene-Disease associations (from GenCC):

long chain acyl-CoA dehydrogenase deficiency
Inheritance: AR Classification: NO_KNOWN Submitted by: ClinGen

ACADL links:

ENSG00000279317 (HGNC:):

ENSG00000279317 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0032475889).

BP6

Variant 2-210195326-T-G is Benign according to our data. Variant chr2-210195326-T-G is described in ClinVar as Benign. ClinVar VariationId is 1620.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001608.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACADL	NM_001608.4	MANE Select	c.997A>C	p.Lys333Gln	missense	Exon 9 of 11	NP_001599.1	P28330

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ACADL	ENST00000233710.4	TSL:1 MANE Select	c.997A>C	p.Lys333Gln	missense	Exon 9 of 11	ENSP00000233710.3	P28330
ACADL	ENST00000862330.1		c.964A>C	p.Lys322Gln	missense	Exon 9 of 11	ENSP00000532389.1
ACADL	ENST00000862329.1		c.859A>C	p.Lys287Gln	missense	Exon 8 of 10	ENSP00000532388.1

Frequencies

GnomAD3 genomes

AF:

0.273

AC:

41476

AN:

152014

Hom.:

6324

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.394

Gnomad AMR

AF:

0.252

Gnomad ASJ

AF:

0.268

Gnomad EAS

AF:

0.206

Gnomad SAS

AF:

0.300

Gnomad FIN

AF:

0.351

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.346

Gnomad OTH

AF:

0.279

GnomAD2 exomes

AF:

0.301

AC:

75355

AN:

250752

AF XY:

0.306

show subpopulations

Gnomad AFR exome

AF:

0.140

Gnomad AMR exome

AF:

0.227

Gnomad ASJ exome

AF:

0.285

Gnomad EAS exome

AF:

0.204

Gnomad FIN exome

AF:

0.358

Gnomad NFE exome

AF:

0.348

Gnomad OTH exome

AF:

0.309

GnomAD4 exome

AF:

0.335

AC:

488328

AN:

1458618

Hom.:

84208

Cov.:

AF XY:

0.335

AC XY:

242788

AN XY:

725766

show subpopulations

African (AFR)

AF:

0.136

AC:

4550

AN:

33430

American (AMR)

AF:

0.228

AC:

10165

AN:

44644

Ashkenazi Jewish (ASJ)

AF:

0.284

AC:

7416

AN:

26112

East Asian (EAS)

AF:

0.199

AC:

7881

AN:

39668

South Asian (SAS)

AF:

0.312

AC:

26859

AN:

86204

European-Finnish (FIN)

AF:

0.366

AC:

19515

AN:

53386

Middle Eastern (MID)

AF:

0.208

AC:

1198

AN:

5754

European-Non Finnish (NFE)

AF:

0.353

AC:

391925

AN:

1109140

Other (OTH)

AF:

0.312

AC:

18819

AN:

60280

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

15384

30769

46153

61538

76922

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12296

24592

36888

49184

61480

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.273

AC:

41472

AN:

152130

Hom.:

6325

Cov.:

AF XY:

0.271

AC XY:

20119

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.142

AC:

5908

AN:

41508

American (AMR)

AF:

0.252

AC:

3843

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.268

AC:

930

AN:

3466

East Asian (EAS)

AF:

0.207

AC:

1072

AN:

5180

South Asian (SAS)

AF:

0.299

AC:

1444

AN:

4828

European-Finnish (FIN)

AF:

0.351

AC:

3709

AN:

10578

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.346

AC:

23556

AN:

67984

Other (OTH)

AF:

0.279

AC:

588

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1518

3037

4555

6074

7592

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

436

872

1308

1744

2180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.319

Hom.:

38081

Bravo

AF:

0.260

TwinsUK

AF:

0.350

AC:

1297

ALSPAC

AF:

0.364

AC:

1402

ESP6500AA

AF:

0.150

AC:

661

ESP6500EA

AF:

0.341

AC:

2936

ExAC

AF:

0.301

AC:

36504

Asia WGS

AF:

0.241

AC:

838

AN:

3478

EpiCase

AF:

0.336

EpiControl

AF:

0.338

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.22

BayesDel_noAF

Uncertain

0.060

CADD

Pathogenic

(source)

DANN

Uncertain

0.99

DEOGEN2

Pathogenic

0.87

Eigen

Uncertain

0.60

Eigen_PC

Uncertain

0.61

FATHMM_MKL

Uncertain

0.96

LIST_S2

Pathogenic

0.99

MetaRNN

Benign

0.0032

MetaSVM

Benign

-1.6

MutationAssessor

Benign

2.0

PhyloP100

7.1

PrimateAI

Uncertain

0.70

PROVEAN

Uncertain

-3.0

REVEL

Uncertain

0.64

Sift

Benign

0.051

Sift4G

Benign

0.071

Polyphen

0.98

Vest4

0.26

MPC

0.85

ClinPred

0.014

GERP RS

5.8

Varity_R

0.63

gMVP

0.92

Mutation Taster

=87/13

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over