Genetic Variant ACACB:c.2144+33_2144+72delTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC (chr12-109188171-CTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001093.4(ACACB):c.2144+33_2144+72delTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000295 in 1,357,024 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000029 ( 0 hom., cov: 0)

Exomes 𝑓: 8.0e-7 ( 0 hom. )

Consequence

ACACB
NM_001093.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.21

Publications

0 publications found

Variant links:

Genes affected

ACACB (HGNC:85): (acetyl-CoA carboxylase beta) Acetyl-CoA carboxylase (ACC) is a complex multifunctional enzyme system. ACC is a biotin-containing enzyme which catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, the rate-limiting step in fatty acid synthesis. ACC-beta is thought to control fatty acid oxidation by means of the ability of malonyl-CoA to inhibit carnitine-palmitoyl-CoA transferase I, the rate-limiting step in fatty acid uptake and oxidation by mitochondria. ACC-beta may be involved in the regulation of fatty acid oxidation, rather than fatty acid biosynthesis. [provided by RefSeq, Oct 2022]

ACACB Gene-Disease associations (from GenCC):

isolated cleft palate
Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACACB links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACACB	NM_001093.4 link	c.2144+33_2144+72delTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC		intron_variant	Intron 13 of 52	ENST00000338432.12	NP_001084.3	O00763-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ACACB	ENST00000338432.12 link	c.2144+10_2144+49delTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT	intron_variant	Intron 13 of 52	1	NM_001093.4	ENSP00000341044.7	O00763-1
ACACB	ENST00000377848.7 link	c.2144+10_2144+49delTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT	intron_variant	Intron 12 of 51	1		ENSP00000367079.3	O00763-1
ACACB	ENST00000377854.9 link	c.-1859+10_-1859+49delTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT	intron_variant	Intron 12 of 46	5		ENSP00000367085.6	F8W8T8

Frequencies

GnomAD3 genomes

AF:

0.0000286

AC:

AN:

105050

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000108

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

7.99e-7

AC:

AN:

1251974

Hom.:

AF XY:

0.00

AC XY:

AN XY:

617866

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

27904

American (AMR)

AF:

0.0000279

AC:

AN:

35894

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21920

East Asian (EAS)

AF:

0.00

AC:

AN:

33178

South Asian (SAS)

AF:

0.00

AC:

AN:

71436

European-Finnish (FIN)

AF:

0.00

AC:

AN:

45274

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4420

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

961366

Other (OTH)

AF:

0.00

AC:

AN:

50582

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0000286

AC:

AN:

105050

Hom.:

Cov.:

AF XY:

0.0000201

AC XY:

AN XY:

49634

show subpopulations

African (AFR)

AF:

0.000108

AC:

AN:

27812

American (AMR)

AF:

0.00

AC:

AN:

10064

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2698

East Asian (EAS)

AF:

0.00

AC:

AN:

3258

South Asian (SAS)

AF:

0.00

AC:

AN:

2426

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6574

Middle Eastern (MID)

AF:

0.00

AC:

AN:

232

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

50024

Other (OTH)

AF:

0.00

AC:

AN:

1316

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.2

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over