rs802036

Variant names:

• chr7-87348578-T-C
• rs802036
• NM_021151.4:c.-21-470T>C

Variant summary

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

The NM_021151.4(CROT):​c.-21-470T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,238 control chromosomes in the GnomAD database, including 1,925 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 0.13 (1925 hom., cov: 32)
• Consequence: CROT NM_021151.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 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.-21-470T>C		intron	N/A	NP_066974.2
	CROT	NM_001143935.2		c.-21-470T>C		intron	N/A	NP_001137407.1
	CROT	NM_001243745.3		c.-21-470T>C		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.-21-470T>C		intron	N/A	ENSP00000331981.4
	CROT	ENST00000412227.6	TSL:1	c.-21-470T>C		intron	N/A	ENSP00000404867.2
	CROT	ENST00000419147.6	TSL:2	c.-21-470T>C		intron	N/A	ENSP00000413575.2

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19034 AN: 152120 Hom.: 1910 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0697

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.000768

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0718

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.125 AC: 19087 AN: 152238 Hom.: 1925 Cov.: 32 AF XY: 0.123 AC XY: 9128 AN XY: 74432

African (AFR) AF: 0.277 AC: 11503 AN: 41488

American (AMR) AF: 0.0696 AC: 1065 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3472

East Asian (EAS) AF: 0.000770 AC: 4 AN: 5194

South Asian (SAS) AF: 0.0288 AC: 139 AN: 4828

European-Finnish (FIN) AF: 0.0888 AC: 942 AN: 10608

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0718 AC: 4884 AN: 68024

Other (OTH) AF: 0.113 AC: 239 AN: 2116

Alfa AF: 0.0832 Hom.: 1277

Bravo AF: 0.131

Asia WGS AF: 0.0400 AC: 139 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.70
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs802036; hg19: chr7-86977894;