rs802024

Positions:

• chr7-87356403-C-T

Variant summary

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

The NM_021151.4(CROT):​c.116-2803C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.049 in 152,134 control chromosomes in the GnomAD database, including 232 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 0.049 (232 hom., cov: 32)
• Consequence: CROT NM_021151.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736

Genes affected

CROT (HGNC:2366): (carnitine O-octanoyltransferase) This gene encodes a member of the carnitine/choline acetyltransferase family. The encoded protein converts 4,8-dimethylnonanoyl-CoA to its corresponding carnitine ester. This transesterification occurs in the peroxisome and is necessary for transport of medium- and long- chain acyl-CoA molecules out of the peroxisome to the cytosol and mitochondria. The protein thus plays a role in lipid metabolism and fatty acid beta-oxidation. Alternatively spliced transcript variants have been described.[provided by RefSeq, Jan 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CROT	NM_021151.4	c.116-2803C>T		intron_variant		ENST00000331536.8
CROT	NM_001143935.2	c.116-1104C>T		intron_variant
CROT	NM_001243745.3	c.116-2803C>T		intron_variant
CROT	XM_011516337.4	c.116-2803C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CROT	ENST00000331536.8	c.116-2803C>T		intron_variant		1	NM_021151.4	P1
CROT	ENST00000412227.6	c.116-2803C>T		intron_variant		1
CROT	ENST00000419147.6	c.116-1104C>T		intron_variant		2
CROT	ENST00000442291.1	c.116-2803C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0489 AC: 7439 AN: 152016 Hom.: 231 Cov.: 32

Gnomad AFR AF: 0.0454

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.00436

Gnomad FIN AF: 0.0755

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0573

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0490 AC: 7448 AN: 152134 Hom.: 232 Cov.: 32 AF XY: 0.0484 AC XY: 3600 AN XY: 74370

Gnomad4 AFR AF: 0.0455

Gnomad4 AMR AF: 0.0324

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.00415

Gnomad4 FIN AF: 0.0755

Gnomad4 NFE AF: 0.0573

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0448 Hom.: 16

Bravo AF: 0.0458

Asia WGS AF: 0.00866 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.68
DANN	Benign	0.31

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: rs802024; hg19: chr7-86985719;