Variant rs470117 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.37 ( 11649 hom., cov: 33)

Exomes 𝑓: 0.45 ( 150309 hom. )

Consequence

CPT1B
NM_152246.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.98

Variant links:

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]

CPT1B links:

CHKB-CPT1B (HGNC:):

CHKB-CPT1B links:

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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 (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/exons	MANE	UniProt
CPT1B	NM_152246.3 linkuse as main transcript	c.1591G>A	p.Glu531Lys	missense_variant	14/20	ENST00000312108.12
CHKB-CPT1B	NR_027928.2 linkuse as main transcript	n.3161G>A		non_coding_transcript_exon_variant	24/30

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPT1B	ENST00000312108.12 linkuse as main transcript	c.1591G>A	p.Glu531Lys	missense_variant	14/20	1	NM_152246.3	P1	Q92523-1

Frequencies

GnomAD3 genomes

AF:

0.366

AC:

55629

AN:

151966

Hom.:

11655

Cov.:

show subpopulations

Gnomad AFR

AF:

0.145

Gnomad AMI

AF:

0.552

Gnomad AMR

AF:

0.424

Gnomad ASJ

AF:

0.429

Gnomad EAS

AF:

0.460

Gnomad SAS

AF:

0.339

Gnomad FIN

AF:

0.453

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.463

Gnomad OTH

AF:

0.384

GnomAD3 exomes

AF:

0.424

AC:

105061

AN:

247692

Hom.:

23301

AF XY:

0.424

AC XY:

56927

AN XY:

134316

show subpopulations

Gnomad AFR exome

AF:

0.137

Gnomad AMR exome

AF:

0.458

Gnomad ASJ exome

AF:

0.437

Gnomad EAS exome

AF:

0.453

Gnomad SAS exome

AF:

0.339

Gnomad FIN exome

AF:

0.457

Gnomad NFE exome

AF:

0.466

Gnomad OTH exome

AF:

0.437

GnomAD4 exome

AF:

0.449

AC:

655949

AN:

1460228

Hom.:

150309

Cov.:

AF XY:

0.446

AC XY:

324157

AN XY:

726472

show subpopulations

Gnomad4 AFR exome

AF:

0.133

Gnomad4 AMR exome

AF:

0.457

Gnomad4 ASJ exome

AF:

0.429

Gnomad4 EAS exome

AF:

0.467

Gnomad4 SAS exome

AF:

0.343

Gnomad4 FIN exome

AF:

0.455

Gnomad4 NFE exome

AF:

0.468

Gnomad4 OTH exome

AF:

0.424

GnomAD4 genome

AF:

0.366

AC:

55630

AN:

152084

Hom.:

11649

Cov.:

AF XY:

0.366

AC XY:

27208

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.145

Gnomad4 AMR

AF:

0.425

Gnomad4 ASJ

AF:

0.429

Gnomad4 EAS

AF:

0.460

Gnomad4 SAS

AF:

0.338

Gnomad4 FIN

AF:

0.453

Gnomad4 NFE

AF:

0.463

Gnomad4 OTH

AF:

0.381

Alfa

AF:

0.432

Hom.:

20207

Bravo

AF:

0.360

TwinsUK

AF:

0.463

AC:

1716

ALSPAC

AF:

0.455

AC:

1755

ESP6500AA

AF:

0.156

AC:

689

ESP6500EA

AF:

0.458

AC:

3935

ExAC

AF:

0.418

AC:

50790

Asia WGS

AF:

0.358

AC:

1243

AN:

3478

EpiCase

AF:

0.450

EpiControl

AF:

0.451

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.090

Cadd

Benign

Dann

Uncertain

1.0

DEOGEN2

Uncertain

0.65

D;D;D;D;.

Eigen

Uncertain

0.26

Eigen_PC

Uncertain

0.30

FATHMM_MKL

Pathogenic

0.98

MetaRNN

Benign

0.0012

T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.5

L;L;L;L;.

MutationTaster

Benign

7.0e-10

P;P;P;P;P;P;P

PrimateAI

Benign

0.46

PROVEAN

Uncertain

-2.5

D;D;D;D;N

REVEL

Uncertain

0.43

Sift

Benign

0.095

T;T;T;T;T

Sift4G

Benign

0.20

T;T;T;T;T

Polyphen

0.68

P;P;P;P;.

Vest4

0.17

ClinPred

0.016

GERP RS

5.3

Varity_R

0.62

gMVP

0.57

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over