Genetic Variant ACBD4:c.*347T>C (chr17-45143918-T-C) – 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.*347T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0535 in 301,424 control chromosomes in the GnomAD database, including 547 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 0.047 ( 231 hom., cov: 32)

Exomes 𝑓: 0.060 ( 316 hom. )

Consequence

ACBD4
NM_001135705.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0240

Publications

10 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=-0.69).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001135705.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ACBD4	NM_001135705.3	MANE Select	c.*347T>C	3_prime_UTR	Exon 10 of 10	NP_001129177.1
ACBD4	NM_001135706.3		c.*277T>C	3_prime_UTR	Exon 10 of 10	NP_001129178.1
ACBD4	NM_001321352.2		c.*277T>C	3_prime_UTR	Exon 12 of 12	NP_001308281.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ACBD4	ENST00000321854.13	TSL:1 MANE Select	c.*347T>C	3_prime_UTR	Exon 10 of 10	ENSP00000314440.8
ACBD4	ENST00000591859.5	TSL:1	c.*277T>C	3_prime_UTR	Exon 12 of 12	ENSP00000465610.1
ACBD4	ENST00000398322.7	TSL:1	c.*347T>C	3_prime_UTR	Exon 9 of 9	ENSP00000381367.2

Frequencies

GnomAD3 genomes

AF:

0.0472

AC:

7173

AN:

151954

Hom.:

232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0118

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0496

Gnomad ASJ

AF:

0.0854

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0700

Gnomad FIN

AF:

0.0292

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0709

Gnomad OTH

AF:

0.0628

GnomAD4 exome

AF:

0.0600

AC:

8954

AN:

149352

Hom.:

316

Cov.:

AF XY:

0.0614

AC XY:

4789

AN XY:

77986

show subpopulations

African (AFR)

AF:

0.0107

AC:

AN:

4208

American (AMR)

AF:

0.0410

AC:

194

AN:

4730

Ashkenazi Jewish (ASJ)

AF:

0.0876

AC:

465

AN:

5308

East Asian (EAS)

AF:

0.000105

AC:

AN:

9520

South Asian (SAS)

AF:

0.0696

AC:

961

AN:

13808

European-Finnish (FIN)

AF:

0.0313

AC:

275

AN:

8788

Middle Eastern (MID)

AF:

0.101

AC:

AN:

786

European-Non Finnish (NFE)

AF:

0.0687

AC:

6374

AN:

92714

Other (OTH)

AF:

0.0590

AC:

560

AN:

9490

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

402

804

1206

1608

2010

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

160

<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:

0.0471

AC:

7169

AN:

152072

Hom.:

231

Cov.:

AF XY:

0.0455

AC XY:

3383

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.0118

AC:

489

AN:

41502

American (AMR)

AF:

0.0494

AC:

756

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0854

AC:

296

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5146

South Asian (SAS)

AF:

0.0702

AC:

339

AN:

4826

European-Finnish (FIN)

AF:

0.0292

AC:

309

AN:

10590

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0709

AC:

4817

AN:

67934

Other (OTH)

AF:

0.0626

AC:

132

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

350

700

1050

1400

1750

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

270

360

450

<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:

0.0607

Hom.:

Bravo

AF:

0.0448

Asia WGS

AF:

0.0280

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

8.2

(source)

DANN

Benign

0.81

PhyloP100

-0.024

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over