rs2924674

chr11-68804309-G-Achr11-68804309-G-Cchr11-68804309-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001876.4(CPT1A):c.454-208C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 152,258 control chromosomes in the GnomAD database, including 64,913 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.92 (64913 hom., cov: 31)
• Consequence: CPT1A NM_001876.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.14

Genes affected

CPT1A (HGNC:2328): (carnitine palmitoyltransferase 1A) The mitochondrial oxidation of long-chain fatty acids is initiated by the sequential action of carnitine palmitoyltransferase I (which is located in the outer membrane and is detergent-labile) and carnitine palmitoyltransferase II (which is located in the inner membrane and is detergent-stable), together with a carnitine-acylcarnitine translocase. CPT I is the key enzyme in the carnitine-dependent transport across the mitochondrial inner membrane and its deficiency results in a decreased rate of fatty acid beta-oxidation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 11-68804309-G-A is Benign according to our data. Variant chr11-68804309-G-A is described in ClinVar as [Benign]. Clinvar id is 678470.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPT1A	NM_001876.4	c.454-208C>T		intron_variant		ENST00000265641.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPT1A	ENST00000265641.10	c.454-208C>T		intron_variant		1	NM_001876.4	P1
CPT1A	ENST00000376618.6	c.454-208C>T		intron_variant		1
CPT1A	ENST00000540367.5	c.454-208C>T		intron_variant		1
CPT1A	ENST00000539743.5	c.454-208C>T		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.920 AC: 139926 AN: 152140 Hom.: 64893 Cov.: 31

Gnomad AFR AF: 0.784

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.915

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.919 AC: 139993 AN: 152258 Hom.: 64913 Cov.: 31 AF XY: 0.920 AC XY: 68495 AN XY: 74442

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.933

Gnomad4 ASJ AF: 0.971

Gnomad4 EAS AF: 0.935

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.984

Gnomad4 OTH AF: 0.916

Alfa AF: 0.971 Hom.: 90954

Bravo AF: 0.911

Asia WGS AF: 0.919 AC: 3199 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.21
Dann	Benign	0.67

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: rs2924674; hg19: chr11-68571777;