Genetic Variant ACSL4:c.1698-10G>A (chrX-109659521-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_001318510.2(ACSL4):c.1698-10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00106 in 1,157,839 control chromosomes in the GnomAD database, including 10 homozygotes. There are 307 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0055 ( 6 hom., 171 hem., cov: 23)

Exomes 𝑓: 0.00058 ( 4 hom. 136 hem. )

Consequence

ACSL4
NM_001318510.2 intron

Scores

Splicing: ADA: 0.00005922

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:3

Conservation

PhyloP100: -1.33

Publications

0 publications found

Variant links:

Genes affected

ACSL4 (HGNC:3571): (acyl-CoA synthetase long chain family member 4) The protein encoded by this gene is an isozyme of the long-chain fatty-acid-coenzyme A ligase family. Although differing in substrate specificity, subcellular localization, and tissue distribution, all isozymes of this family convert free long-chain fatty acids into fatty acyl-CoA esters, and thereby play a key role in lipid biosynthesis and fatty acid degradation. This isozyme preferentially utilizes arachidonate as substrate. The absence of this enzyme may contribute to the cognitive disability or Alport syndrome. Alternative splicing of this gene generates multiple transcript variants. [provided by RefSeq, Jan 2016]

ACSL4 Gene-Disease associations (from GenCC):

non-syndromic X-linked intellectual disability
Inheritance: XL Classification: DEFINITIVE, MODERATE, SUPPORTIVE Submitted by: ClinGen, Illumina, Orphanet
intellectual disability, X-linked 63
Inheritance: XL Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P

ACSL4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant X-109659521-C-T is Benign according to our data. Variant chrX-109659521-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 434072.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00553 (615/111112) while in subpopulation AFR AF = 0.0172 (527/30647). AF 95% confidence interval is 0.016. There are 6 homozygotes in GnomAd4. There are 171 alleles in the male GnomAd4 subpopulation. Median coverage is 23. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 6 XL gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318510.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ACSL4	NM_001318510.2	MANE Select	c.1698-10G>A	intron	N/A	NP_001305439.1
ACSL4	NM_001318509.2		c.1821-10G>A	intron	N/A	NP_001305438.1
ACSL4	NM_001437245.1		c.1821-10G>A	intron	N/A	NP_001424174.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ACSL4	ENST00000672401.1	MANE Select	c.1698-10G>A	intron	N/A	ENSP00000500273.1
ACSL4	ENST00000348502.10	TSL:1	c.1698-10G>A	intron	N/A	ENSP00000262835.7
ACSL4	ENST00000340800.7	TSL:5	c.1821-10G>A	intron	N/A	ENSP00000339787.2

Frequencies

GnomAD3 genomes

AF:

0.00538

AC:

597

AN:

111063

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0169

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00612

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000562

Gnomad SAS

AF:

0.00188

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00420

Gnomad NFE

AF:

0.0000189

Gnomad OTH

AF:

0.00403

GnomAD2 exomes

AF:

0.00149

AC:

270

AN:

180881

AF XY:

0.00101

show subpopulations

Gnomad AFR exome

AF:

0.0184

Gnomad AMR exome

AF:

0.000812

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000247

Gnomad OTH exome

AF:

0.000674

GnomAD4 exome

AF:

0.000585

AC:

612

AN:

1046727

Hom.:

Cov.:

AF XY:

0.000425

AC XY:

136

AN XY:

319693

show subpopulations

African (AFR)

AF:

0.0174

AC:

441

AN:

25398

American (AMR)

AF:

0.00177

AC:

AN:

34959

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18993

East Asian (EAS)

AF:

0.00

AC:

AN:

29913

South Asian (SAS)

AF:

0.000246

AC:

AN:

52839

European-Finnish (FIN)

AF:

0.0000250

AC:

AN:

40045

Middle Eastern (MID)

AF:

0.000747

AC:

AN:

4018

European-Non Finnish (NFE)

AF:

0.00000377

AC:

AN:

796171

Other (OTH)

AF:

0.00200

AC:

AN:

44391

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

111

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.00553

AC:

615

AN:

111112

Hom.:

Cov.:

AF XY:

0.00511

AC XY:

171

AN XY:

33480

show subpopulations

African (AFR)

AF:

0.0172

AC:

527

AN:

30647

American (AMR)

AF:

0.00611

AC:

AN:

10479

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2626

East Asian (EAS)

AF:

0.000564

AC:

AN:

3547

South Asian (SAS)

AF:

0.00189

AC:

AN:

2652

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5963

Middle Eastern (MID)

AF:

0.00463

AC:

AN:

216

European-Non Finnish (NFE)

AF:

0.0000189

AC:

AN:

52794

Other (OTH)

AF:

0.00995

AC:

AN:

1507

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

105

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.00286

Hom.:

Bravo

AF:

0.00682

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:3

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Non-syndromic X-linked intellectual disability

Uncertain:1

Aug 31, 2011

Center for Human Genetics, Inc, Center for Human Genetics, Inc

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

not specified

Benign:1

Dec 17, 2016

Genetic Services Laboratory, University of Chicago

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

ACSL4-related disorder

Benign:1

Jun 11, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

not provided

Benign:1

Dec 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.20

(source)

DANN

Benign

0.15

PhyloP100

-1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000059

dbscSNV1_RF

Benign

0.0

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

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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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over