rs802026

Variant names:

• chr7-87359723-G-A
• rs802026
• ENST00000412227.6:c.*369G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-87359723-G-A
• chr7-87359723-G-T

Variant summary

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

The NM_001243745.3(CROT):​c.*369G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 1,013,456 control chromosomes in the GnomAD database, including 7,477 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 0.14 (1975 hom., cov: 32)
  • Exomes 𝑓: 0.11 (5502 hom.)
• Consequence: CROT NM_001243745.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.745

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CROT	NM_021151.4	c.240+393G>A		intron_variant	Intron 4 of 17	ENST00000331536.8	NP_066974.2
CROT	NM_001243745.3	c.*369G>A		3_prime_UTR_variant	Exon 4 of 4		NP_001230674.1
CROT	NM_001143935.2	c.324+393G>A		intron_variant	Intron 5 of 18		NP_001137407.1
CROT	XM_011516337.4	c.240+393G>A		intron_variant	Intron 4 of 17		XP_011514639.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CROT	ENST00000412227.6	c.*369G>A		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000404867.2
CROT	ENST00000331536.8	c.240+393G>A		intron_variant	Intron 4 of 17	1	NM_021151.4	ENSP00000331981.4
CROT	ENST00000419147.6	c.324+393G>A		intron_variant	Intron 5 of 18	2		ENSP00000413575.2
CROT	ENST00000442291.1	c.240+393G>A		intron_variant	Intron 3 of 16	5		ENSP00000411983.1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22014 AN: 152042 Hom.: 1972 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.109 AC: 94063 AN: 861296 Hom.: 5502 Cov.: 23 AF XY: 0.110 AC XY: 43765 AN XY: 399110

Gnomad4 AFR exome AF: 0.257

Gnomad4 AMR exome AF: 0.108

Gnomad4 ASJ exome AF: 0.120

Gnomad4 EAS exome AF: 0.0199

Gnomad4 SAS exome AF: 0.150

Gnomad4 FIN exome AF: 0.103

Gnomad4 NFE exome AF: 0.105

Gnomad4 OTH exome AF: 0.114

GnomAD4 genome AF: 0.145 AC: 22056 AN: 152160 Hom.: 1975 Cov.: 32 AF XY: 0.144 AC XY: 10685 AN XY: 74382

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0177

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.132

Alfa AF: 0.108 Hom.: 2005

Bravo AF: 0.146

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.44

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: rs802026; hg19: chr7-86989039;