rs1075453

chr19-49691142-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPT1C	NM_001199753.2	c.-282G>C		5_prime_UTR_variant	1/20	ENST00000598293.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPT1C	ENST00000598293.6	c.-282G>C		5_prime_UTR_variant	1/20	2	NM_001199753.2	P1

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64429 AN: 151290 Hom.: 14273 Cov.: 28

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: 17 AN: 62 Hom.: 3 Cov.: 0 AF XY: 0.200 AC XY: 10 AN XY: 50

Gnomad4 AFR exome AF: 1.00

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.237

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.426 AC: 64513 AN: 151408 Hom.: 14308 Cov.: 28 AF XY: 0.419 AC XY: 30982 AN XY: 74000

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.430

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	12
Dann	Benign	0.87

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

Other links and lift over

dbSNP: rs1075453; hg19: chr19-50194399;