dbSNP rs1075453: CPT1C:c.-282G>C (chr19-49691142-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001199753.2(CPT1C):c.-282G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,470 control chromosomes in the GnomAD database, including 14,311 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 0.43 ( 14308 hom., cov: 28)

Exomes 𝑓: 0.27 ( 3 hom. )

Consequence

CPT1C
NM_001199753.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.257

Publications

7 publications found

Variant links:

Genes affected

CPT1C (HGNC:18540): (carnitine palmitoyltransferase 1C) This gene encodes a member of the carnitine/choline acetyltransferase family. The encoded protein regulates the beta-oxidation and transport of long-chain fatty acids into mitochondria, and may play a role in the regulation of feeding behavior and whole-body energy homeostasis. Alternatively spliced transcript variants encoding multiple protein isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]

CPT1C Gene-Disease associations (from GenCC):

hereditary spastic paraplegia 73
Inheritance: AD Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics
hereditary spastic paraplegia
Inheritance: AD Classification: LIMITED Submitted by: ClinGen

CPT1C links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001199753.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CPT1C	NM_001199753.2	MANE Select	c.-282G>C	5_prime_UTR	Exon 1 of 20	NP_001186682.1
CPT1C	NR_108072.2		n.27G>C	non_coding_transcript_exon	Exon 1 of 21
CPT1C	NM_001378482.1		c.-282G>C	5_prime_UTR	Exon 1 of 19	NP_001365411.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CPT1C	ENST00000598293.6	TSL:2 MANE Select	c.-282G>C	5_prime_UTR	Exon 1 of 20	ENSP00000473028.1
CPT1C	ENST00000323446.9	TSL:1	c.-213G>C	5_prime_UTR	Exon 1 of 19	ENSP00000319343.4
CPT1C	ENST00000598259.5	TSL:2	n.-323G>C	non_coding_transcript_exon	Exon 1 of 20	ENSP00000472742.1

Frequencies

GnomAD3 genomes

AF:

0.426

AC:

64429

AN:

151290

Hom.:

14273

Cov.:

show subpopulations

Gnomad AFR

AF:

0.557

Gnomad AMI

AF:

0.412

Gnomad AMR

AF:

0.391

Gnomad ASJ

AF:

0.375

Gnomad EAS

AF:

0.260

Gnomad SAS

AF:

0.334

Gnomad FIN

AF:

0.349

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.388

Gnomad OTH

AF:

0.425

GnomAD4 exome

AF:

0.274

AC:

AN:

Hom.:

Cov.:

AF XY:

0.200

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.237

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.426

AC:

64513

AN:

151408

Hom.:

14308

Cov.:

AF XY:

0.419

AC XY:

30982

AN XY:

74000

show subpopulations

African (AFR)

AF:

0.558

AC:

22955

AN:

41168

American (AMR)

AF:

0.391

AC:

5935

AN:

15196

Ashkenazi Jewish (ASJ)

AF:

0.375

AC:

1300

AN:

3468

East Asian (EAS)

AF:

0.260

AC:

1341

AN:

5150

South Asian (SAS)

AF:

0.332

AC:

1587

AN:

4786

European-Finnish (FIN)

AF:

0.349

AC:

3666

AN:

10506

Middle Eastern (MID)

AF:

0.520

AC:

153

AN:

294

European-Non Finnish (NFE)

AF:

0.388

AC:

26300

AN:

67832

Other (OTH)

AF:

0.430

AC:

902

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1742

3483

5225

6966

8708

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

588

1176

1764

2352

2940

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.405

Hom.:

1615

Bravo

AF:

0.441

Asia WGS

AF:

0.391

AC:

1358

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

(source)

DANN

Benign

0.87

PhyloP100

-0.26

PromoterAI

-0.041

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over