NM_021151.4:c.116-1890C>T

Variant names:

• chr7-87357316-C-T
• rs802025
• NM_021151.4:c.116-1890C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021151.4(CROT):​c.116-1890C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0553 in 152,136 control chromosomes in the GnomAD database, including 303 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 0.055 (303 hom., cov: 31)
• Consequence: CROT NM_021151.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 3 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0663 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021151.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CROT	NM_021151.4	MANE Select	c.116-1890C>T		intron	N/A	NP_066974.2
	CROT	NM_001143935.2		c.116-191C>T		intron	N/A	NP_001137407.1
	CROT	NM_001243745.3		c.116-1890C>T		intron	N/A	NP_001230674.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CROT	ENST00000331536.8	TSL:1 MANE Select	c.116-1890C>T		intron	N/A	ENSP00000331981.4
	CROT	ENST00000412227.6	TSL:1	c.116-1890C>T		intron	N/A	ENSP00000404867.2
	CROT	ENST00000419147.6	TSL:2	c.116-191C>T		intron	N/A	ENSP00000413575.2

Frequencies

GnomAD3 genomes AF: 0.0553 AC: 8407 AN: 152018 Hom.: 301 Cov.: 31

Gnomad AFR AF: 0.0682

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.0488

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.00435

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0573

Gnomad OTH AF: 0.0552

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

GnomAD4 genome AF: 0.0553 AC: 8420 AN: 152136 Hom.: 303 Cov.: 31 AF XY: 0.0548 AC XY: 4073 AN XY: 74386

African (AFR) AF: 0.0684 AC: 2837 AN: 41500

American (AMR) AF: 0.0338 AC: 517 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0488 AC: 169 AN: 3464

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5170

South Asian (SAS) AF: 0.00414 AC: 20 AN: 4826

European-Finnish (FIN) AF: 0.0753 AC: 796 AN: 10578

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0573 AC: 3894 AN: 67992

Other (OTH) AF: 0.0546 AC: 115 AN: 2106

Alfa AF: 0.0180 Hom.: 8

Bravo AF: 0.0532

Asia WGS AF: 0.00953 AC: 33 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.35
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs802025; hg19: chr7-86986632;