Genetic Variant NM_001135705.3:c.650-107C>T (chr17-45138914-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001135705.3(ACBD4):c.650-107C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 1,208,418 control chromosomes in the GnomAD database, including 86,657 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.44 ( 15766 hom., cov: 32)

Exomes 𝑓: 0.36 ( 70891 hom. )

Consequence

ACBD4
NM_001135705.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11

Publications

63 publications found

Variant links:

Genes affected

ACBD4 (HGNC:23337): (acyl-CoA binding domain containing 4) This gene encodes a member of the acyl-coenzyme A binding domain containing protein family. All family members contain the conserved acyl-Coenzyme A binding domain, which binds acyl-CoA thiol esters. They are thought to play roles in acyl-CoA dependent lipid metabolism. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]

ACBD4 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACBD4	NM_001135705.3 link	c.650-107C>T		intron_variant	Intron 8 of 9	ENST00000321854.13	NP_001129177.1	Q8NC06-2A0A0S2Z5Q0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACBD4	ENST00000321854.13 link	c.650-107C>T		intron_variant	Intron 8 of 9	1	NM_001135705.3	ENSP00000314440.8		Q8NC06-2
ACBD4	ENST00000591859.5 link	c.688-107C>T		intron_variant	Intron 10 of 11	1		ENSP00000465610.1		Q8NC06-3

Frequencies

GnomAD3 genomes

AF:

0.438

AC:

66563

AN:

151980

Hom.:

15746

Cov.:

show subpopulations

Gnomad AFR

AF:

0.617

Gnomad AMI

AF:

0.319

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.388

Gnomad EAS

AF:

0.454

Gnomad SAS

AF:

0.380

Gnomad FIN

AF:

0.403

Gnomad MID

AF:

0.462

Gnomad NFE

AF:

0.342

Gnomad OTH

AF:

0.409

GnomAD4 exome

AF:

0.361

AC:

381328

AN:

1056320

Hom.:

70891

AF XY:

0.360

AC XY:

191476

AN XY:

531994

show subpopulations

African (AFR)

AF:

0.634

AC:

16121

AN:

25414

American (AMR)

AF:

0.435

AC:

14530

AN:

33406

Ashkenazi Jewish (ASJ)

AF:

0.381

AC:

8150

AN:

21390

East Asian (EAS)

AF:

0.436

AC:

15106

AN:

34616

South Asian (SAS)

AF:

0.362

AC:

25440

AN:

70360

European-Finnish (FIN)

AF:

0.375

AC:

13238

AN:

35322

Middle Eastern (MID)

AF:

0.408

AC:

1382

AN:

3390

European-Non Finnish (NFE)

AF:

0.343

AC:

269480

AN:

785946

Other (OTH)

AF:

0.385

AC:

17881

AN:

46476

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

12225

24450

36676

48901

61126

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7822

15644

23466

31288

39110

<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:

0.438

AC:

66629

AN:

152098

Hom.:

15766

Cov.:

AF XY:

0.441

AC XY:

32782

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.617

AC:

25587

AN:

41488

American (AMR)

AF:

0.439

AC:

6712

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.388

AC:

1344

AN:

3466

East Asian (EAS)

AF:

0.454

AC:

2344

AN:

5168

South Asian (SAS)

AF:

0.379

AC:

1828

AN:

4826

European-Finnish (FIN)

AF:

0.403

AC:

4260

AN:

10582

Middle Eastern (MID)

AF:

0.455

AC:

133

AN:

292

European-Non Finnish (NFE)

AF:

0.342

AC:

23269

AN:

67960

Other (OTH)

AF:

0.408

AC:

861

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1840

3680

5519

7359

9199

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

594

1188

1782

2376

2970

<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:

0.378

Hom.:

48101

Bravo

AF:

0.452

Asia WGS

AF:

0.443

AC:

1539

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.038

(source)

DANN

Benign

0.33

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over