chr7-87364235-C-G

Variant names:

• chr7-87364235-C-G
• rs802030
• NM_021151.4:c.547+2383C>G

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+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
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 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+2383C>G		intron	N/A	NP_066974.2
	CROT	NM_001143935.2		c.631+2383C>G		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+2383C>G		intron	N/A	ENSP00000331981.4	Q9UKG9-1
	CROT	ENST00000419147.6	TSL:2	c.631+2383C>G		intron	N/A	ENSP00000413575.2	Q9UKG9-3
	CROT	ENST00000881400.1		c.547+2383C>G		intron	N/A	ENSP00000551459.1

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

African (AFR) AF: 0.345 AC: 14301 AN: 41464

American (AMR) AF: 0.116 AC: 1768 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3472

East Asian (EAS) AF: 0.0176 AC: 91 AN: 5182

South Asian (SAS) AF: 0.158 AC: 764 AN: 4824

European-Finnish (FIN) AF: 0.108 AC: 1145 AN: 10588

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7373 AN: 67982

Other (OTH) AF: 0.153 AC: 323 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.36
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: rs802030; hg19: chr7-86993551;