NM_021151.4:c.547+507C>T

Variant names:

• chr7-87362359-C-T
• rs802028
• NM_021151.4:c.547+507C>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.547+507C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 145,318 control chromosomes in the GnomAD database, including 2,239 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 0.16 (2239 hom., cov: 28)
• Consequence: CROT NM_021151.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 2 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CROT	NM_021151.4	MANE Select	c.547+507C>T		intron	N/A	NP_066974.2
	CROT	NM_001143935.2		c.631+507C>T		intron	N/A	NP_001137407.1	Q9UKG9-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CROT	ENST00000331536.8	TSL:1 MANE Select	c.547+507C>T		intron	N/A	ENSP00000331981.4	Q9UKG9-1
	CROT	ENST00000419147.6	TSL:2	c.631+507C>T		intron	N/A	ENSP00000413575.2	Q9UKG9-3
	CROT	ENST00000881400.1		c.547+507C>T		intron	N/A	ENSP00000551459.1

Frequencies

GnomAD3 genomes AF: 0.157 AC: 22733 AN: 145238 Hom.: 2232 Cov.: 28

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0182

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.151

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.157 AC: 22779 AN: 145318 Hom.: 2239 Cov.: 28 AF XY: 0.156 AC XY: 10964 AN XY: 70182

African (AFR) AF: 0.285 AC: 11133 AN: 39058

American (AMR) AF: 0.113 AC: 1620 AN: 14292

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 437 AN: 3432

East Asian (EAS) AF: 0.0181 AC: 88 AN: 4868

South Asian (SAS) AF: 0.160 AC: 735 AN: 4588

European-Finnish (FIN) AF: 0.115 AC: 1034 AN: 8978

Middle Eastern (MID) AF: 0.158 AC: 41 AN: 260

European-Non Finnish (NFE) AF: 0.109 AC: 7287 AN: 66934

Other (OTH) AF: 0.139 AC: 279 AN: 2006

Alfa AF: 0.0586 Hom.: 60

Bravo AF: 0.157

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.60
PhyloP100		-1.1
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: rs802028; hg19: chr7-86991675;