rs802030

chr7-87364235-C-G

Variant summary

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

The NM_021151.4(CROT):c.547+2383C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,110 control chromosomes in the GnomAD database, including 3,258 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 0.17 (3258 hom., cov: 32)
• Consequence: CROT NM_021151.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CROT	NM_021151.4	c.547+2383C>G		intron_variant		ENST00000331536.8
CROT	NM_001143935.2	c.631+2383C>G		intron_variant
CROT	XM_011516337.4	c.547+2383C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CROT	ENST00000331536.8	c.547+2383C>G		intron_variant		1	NM_021151.4	P1
CROT	ENST00000419147.6	c.631+2383C>G		intron_variant		2
CROT	ENST00000442291.1	c.547+2383C>G		intron_variant		5
CROT	ENST00000488850.1	n.254+2383C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26321 AN: 151992 Hom.: 3232 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.174 AC: 26403 AN: 152110 Hom.: 3258 Cov.: 32 AF XY: 0.172 AC XY: 12757 AN XY: 74378

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0176

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.153

Alfa AF: 0.143 Hom.: 271

Bravo AF: 0.179

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.14
Dann	Benign	0.36

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: rs802030; hg19: chr7-86993551;