rs2268388

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001093.4(ACACB):​c.2914-870G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,006 control chromosomes in the GnomAD database, including 1,593 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 0.14 ( 1593 hom., cov: 31)

Consequence

ACACB
NM_001093.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.681
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ACACBNM_001093.4 linkuse as main transcriptc.2914-870G>A intron_variant ENST00000338432.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ACACBENST00000338432.12 linkuse as main transcriptc.2914-870G>A intron_variant 1 NM_001093.4 P1O00763-1
ACACBENST00000377848.7 linkuse as main transcriptc.2914-870G>A intron_variant 1 P1O00763-1
ACACBENST00000377854.9 linkuse as main transcriptc.-1089-870G>A intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.141
AC:
21381
AN:
151888
Hom.:
1587
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.131
Gnomad AMI
AF:
0.0374
Gnomad AMR
AF:
0.123
Gnomad ASJ
AF:
0.113
Gnomad EAS
AF:
0.225
Gnomad SAS
AF:
0.176
Gnomad FIN
AF:
0.134
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.146
Gnomad OTH
AF:
0.140
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.141
AC:
21407
AN:
152006
Hom.:
1593
Cov.:
31
AF XY:
0.140
AC XY:
10370
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.131
Gnomad4 AMR
AF:
0.122
Gnomad4 ASJ
AF:
0.113
Gnomad4 EAS
AF:
0.225
Gnomad4 SAS
AF:
0.176
Gnomad4 FIN
AF:
0.134
Gnomad4 NFE
AF:
0.146
Gnomad4 OTH
AF:
0.144
Alfa
AF:
0.146
Hom.:
1649
Bravo
AF:
0.141
Asia WGS
AF:
0.213
AC:
742
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.89
DANN
Benign
0.44

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2268388; hg19: chr12-109643645; API