rs470117
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152246.3(CPT1B):c.1591G>A(p.Glu531Lys) variant causes a missense change. The variant allele was found at a frequency of 0.441 in 1,612,312 control chromosomes in the GnomAD database, including 161,958 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 0.37 ( 11649 hom., cov: 33)
Exomes 𝑓: 0.45 ( 150309 hom. )
Consequence
CPT1B
NM_152246.3 missense
NM_152246.3 missense
Scores
1
6
11
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.98
Publications
49 publications found
Genes affected
CPT1B (HGNC:2329): (carnitine palmitoyltransferase 1B) The protein encoded by this gene, a member of the carnitine/choline acetyltransferase family, is the rate-controlling enzyme of the long-chain fatty acid beta-oxidation pathway in muscle mitochondria. This enzyme is required for the net transport of long-chain fatty acyl-CoAs from the cytoplasm into the mitochondria. Multiple transcript variants encoding different isoforms have been found for this gene, and read-through transcripts are expressed from the upstream locus that include exons from this gene. [provided by RefSeq, Jun 2009]
CHKB-CPT1B (HGNC:41998): (CHKB-CPT1B readthrough (NMD candidate)) The genes CHKB and CPT1B are adjacent on chromosome 22 and read-through transcripts are expressed that include exons from both loci. The read-through transcripts are candidates for nonsense-mediated mRNA decay (NMD) and are unlikely to express proteins. [provided by RefSeq, Jun 2009]
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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 (MetaRNN=0.001192987).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPT1B | NM_152246.3 | c.1591G>A | p.Glu531Lys | missense_variant | Exon 14 of 20 | ENST00000312108.12 | NP_689452.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPT1B | ENST00000312108.12 | c.1591G>A | p.Glu531Lys | missense_variant | Exon 14 of 20 | 1 | NM_152246.3 | ENSP00000312189.8 | ||
CHKB-CPT1B | ENST00000453634.5 | n.*1816G>A | non_coding_transcript_exon_variant | Exon 17 of 23 | 5 | ENSP00000457031.1 | ||||
CHKB-CPT1B | ENST00000453634.5 | n.*1816G>A | 3_prime_UTR_variant | Exon 17 of 23 | 5 | ENSP00000457031.1 |
Frequencies
GnomAD3 genomes AF: 0.366 AC: 55629AN: 151966Hom.: 11655 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
55629
AN:
151966
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.424 AC: 105061AN: 247692 AF XY: 0.424 show subpopulations
GnomAD2 exomes
AF:
AC:
105061
AN:
247692
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.449 AC: 655949AN: 1460228Hom.: 150309 Cov.: 59 AF XY: 0.446 AC XY: 324157AN XY: 726472 show subpopulations
GnomAD4 exome
AF:
AC:
655949
AN:
1460228
Hom.:
Cov.:
59
AF XY:
AC XY:
324157
AN XY:
726472
show subpopulations
African (AFR)
AF:
AC:
4451
AN:
33474
American (AMR)
AF:
AC:
20416
AN:
44710
Ashkenazi Jewish (ASJ)
AF:
AC:
11220
AN:
26126
East Asian (EAS)
AF:
AC:
18519
AN:
39696
South Asian (SAS)
AF:
AC:
29619
AN:
86248
European-Finnish (FIN)
AF:
AC:
23627
AN:
51956
Middle Eastern (MID)
AF:
AC:
1972
AN:
5764
European-Non Finnish (NFE)
AF:
AC:
520515
AN:
1111880
Other (OTH)
AF:
AC:
25610
AN:
60374
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.480
Heterozygous variant carriers
0
20746
41493
62239
82986
103732
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.366 AC: 55630AN: 152084Hom.: 11649 Cov.: 33 AF XY: 0.366 AC XY: 27208AN XY: 74342 show subpopulations
GnomAD4 genome
AF:
AC:
55630
AN:
152084
Hom.:
Cov.:
33
AF XY:
AC XY:
27208
AN XY:
74342
show subpopulations
African (AFR)
AF:
AC:
6013
AN:
41528
American (AMR)
AF:
AC:
6492
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
1487
AN:
3468
East Asian (EAS)
AF:
AC:
2375
AN:
5164
South Asian (SAS)
AF:
AC:
1632
AN:
4828
European-Finnish (FIN)
AF:
AC:
4790
AN:
10566
Middle Eastern (MID)
AF:
AC:
94
AN:
294
European-Non Finnish (NFE)
AF:
AC:
31441
AN:
67940
Other (OTH)
AF:
AC:
804
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
1749
3498
5247
6996
8745
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
1716
ALSPAC
AF:
AC:
1755
ESP6500AA
AF:
AC:
689
ESP6500EA
AF:
AC:
3935
ExAC
AF:
AC:
50790
Asia WGS
AF:
AC:
1243
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D;D;D;D;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
.;.;.;T;T
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L;L;.
PhyloP100
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D;D;N
REVEL
Uncertain
Sift
Benign
T;T;T;T;T
Sift4G
Benign
T;T;T;T;T
Polyphen
P;P;P;P;.
Vest4
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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