17-37132758-G-A

Variant summary

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

The NM_198834.3(ACACA):​c.5680-2540C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,072 control chromosomes in the GnomAD database, including 3,043 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 0.18 ( 3043 hom., cov: 32)

Consequence

ACACA
NM_198834.3 intron

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.179
Variant links:
Genes affected
ACACA (HGNC:84): (acetyl-CoA carboxylase alpha) 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. There are two ACC forms, alpha and beta, encoded by two different genes. ACC-alpha is highly enriched in lipogenic tissues. The enzyme is under long term control at the transcriptional and translational levels and under short term regulation by the phosphorylation/dephosphorylation of targeted serine residues and by allosteric transformation by citrate or palmitoyl-CoA. Multiple alternatively spliced transcript variants divergent in the 5' sequence and encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ACACANM_198834.3 linkuse as main transcriptc.5680-2540C>T intron_variant ENST00000616317.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ACACAENST00000616317.5 linkuse as main transcriptc.5680-2540C>T intron_variant 1 NM_198834.3 Q13085-4

Frequencies

GnomAD3 genomes
AF:
0.179
AC:
27144
AN:
151954
Hom.:
3045
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0722
Gnomad AMI
AF:
0.0813
Gnomad AMR
AF:
0.189
Gnomad ASJ
AF:
0.147
Gnomad EAS
AF:
0.456
Gnomad SAS
AF:
0.377
Gnomad FIN
AF:
0.288
Gnomad MID
AF:
0.215
Gnomad NFE
AF:
0.191
Gnomad OTH
AF:
0.185
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.179
AC:
27154
AN:
152072
Hom.:
3043
Cov.:
32
AF XY:
0.187
AC XY:
13933
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.0721
Gnomad4 AMR
AF:
0.190
Gnomad4 ASJ
AF:
0.147
Gnomad4 EAS
AF:
0.456
Gnomad4 SAS
AF:
0.377
Gnomad4 FIN
AF:
0.288
Gnomad4 NFE
AF:
0.191
Gnomad4 OTH
AF:
0.188
Alfa
AF:
0.193
Hom.:
5093
Bravo
AF:
0.164

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.28

Splicing

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: rs7208415; hg19: chr17-35489683; API