12-109188171-CTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT-CTCCTTCCTTCCTTCCTTCCT

Variant names:

• chr12-109188171-CTCCTTCCTTCCTTCCTTCCT-C
• rs373209583
• NM_001093.4:c.2144+53_2144+72delTTCCTTCCTTCCTTCCTTCC

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_001093.4(ACACB):​c.2144+53_2144+72delTTCCTTCCTTCCTTCCTTCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00379 in 1,357,006 control chromosomes in the GnomAD database, including 62 homozygotes. 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. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.017 (36 hom., cov: 0)
  • Exomes 𝑓: 0.0027 (26 hom.)
• Consequence: ACACB NM_001093.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.21
• Publications: 0 publications found

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)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 12-109188171-CTCCTTCCTTCCTTCCTTCCT-C is Benign according to our data. Variant chr12-109188171-CTCCTTCCTTCCTTCCTTCCT-C is described in ClinVar as Benign. ClinVar VariationId is 771459.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0171 (1796/105134) while in subpopulation AFR AF = 0.0468 (1307/27902). AF 95% confidence interval is 0.0447. There are 36 homozygotes in GnomAd4. There are 886 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 36 Unknown gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACACB	NM_001093.4	c.2144+53_2144+72delTTCCTTCCTTCCTTCCTTCC		intron_variant	Intron 13 of 52	ENST00000338432.12	NP_001084.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACACB	ENST00000338432.12	c.2144+10_2144+29delTCCTTCCTTCCTTCCTTCCT		intron_variant	Intron 13 of 52	1	NM_001093.4	ENSP00000341044.7
ACACB	ENST00000377848.7	c.2144+10_2144+29delTCCTTCCTTCCTTCCTTCCT		intron_variant	Intron 12 of 51	1		ENSP00000367079.3
ACACB	ENST00000377854.9	c.-1859+10_-1859+29delTCCTTCCTTCCTTCCTTCCT		intron_variant	Intron 12 of 46	5		ENSP00000367085.6

Frequencies

GnomAD3 genomes AF: 0.0171 AC: 1792 AN: 105044 Hom.: 36 Cov.: 0

Gnomad AFR AF: 0.0469

Gnomad AMI AF: 0.00619

Gnomad AMR AF: 0.0126

Gnomad ASJ AF: 0.000741

Gnomad EAS AF: 0.00583

Gnomad SAS AF: 0.00247

Gnomad FIN AF: 0.0190

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00382

Gnomad OTH AF: 0.0114

GnomAD4 exome AF: 0.00267 AC: 3345 AN: 1251872 Hom.: 26 AF XY: 0.00269 AC XY: 1663 AN XY: 617824

African (AFR) AF: 0.0264 AC: 734 AN: 27840

American (AMR) AF: 0.00295 AC: 106 AN: 35890

Ashkenazi Jewish (ASJ) AF: 0.000228 AC: 5 AN: 21918

East Asian (EAS) AF: 0.00639 AC: 212 AN: 33174

South Asian (SAS) AF: 0.000630 AC: 45 AN: 71430

European-Finnish (FIN) AF: 0.0128 AC: 579 AN: 45270

Middle Eastern (MID) AF: 0.00181 AC: 8 AN: 4420

European-Non Finnish (NFE) AF: 0.00150 AC: 1442 AN: 961358

Other (OTH) AF: 0.00423 AC: 214 AN: 50572

GnomAD4 genome AF: 0.0171 AC: 1796 AN: 105134 Hom.: 36 Cov.: 0 AF XY: 0.0178 AC XY: 886 AN XY: 49734

African (AFR) AF: 0.0468 AC: 1307 AN: 27902

American (AMR) AF: 0.0126 AC: 127 AN: 10078

Ashkenazi Jewish (ASJ) AF: 0.000741 AC: 2 AN: 2698

East Asian (EAS) AF: 0.00585 AC: 19 AN: 3246

South Asian (SAS) AF: 0.00247 AC: 6 AN: 2432

European-Finnish (FIN) AF: 0.0190 AC: 125 AN: 6576

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 210

European-Non Finnish (NFE) AF: 0.00382 AC: 191 AN: 50016

Other (OTH) AF: 0.0113 AC: 15 AN: 1330

Alfa AF: 0.00 Hom.: 759

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 28, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs373209583; hg19: chr12-109625976;