chr7-87356403-C-T

Variant names:

• chr7-87356403-C-T
• rs802024
• NM_021151.4:c.116-2803C>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.116-2803C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.049 in 152,134 control chromosomes in the GnomAD database, including 232 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 0.049 (232 hom., cov: 32)
• Consequence: CROT NM_021151.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CROT	NM_021151.4	c.116-2803C>T		intron_variant	Intron 3 of 17	ENST00000331536.8	NP_066974.2
CROT	NM_001143935.2	c.116-1104C>T		intron_variant	Intron 3 of 18		NP_001137407.1
CROT	NM_001243745.3	c.116-2803C>T		intron_variant	Intron 3 of 3		NP_001230674.1
CROT	XM_011516337.4	c.116-2803C>T		intron_variant	Intron 3 of 17		XP_011514639.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CROT	ENST00000331536.8	c.116-2803C>T		intron_variant	Intron 3 of 17	1	NM_021151.4	ENSP00000331981.4
CROT	ENST00000412227.6	c.116-2803C>T		intron_variant	Intron 3 of 3	1		ENSP00000404867.2
CROT	ENST00000419147.6	c.116-1104C>T		intron_variant	Intron 3 of 18	2		ENSP00000413575.2
CROT	ENST00000442291.1	c.116-2803C>T		intron_variant	Intron 2 of 16	5		ENSP00000411983.1

Frequencies

GnomAD3 genomes AF: 0.0489 AC: 7439 AN: 152016 Hom.: 231 Cov.: 32

Gnomad AFR AF: 0.0454

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.00436

Gnomad FIN AF: 0.0755

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0573

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0490 AC: 7448 AN: 152134 Hom.: 232 Cov.: 32 AF XY: 0.0484 AC XY: 3600 AN XY: 74370

African (AFR) AF: 0.0455 AC: 1890 AN: 41496

American (AMR) AF: 0.0324 AC: 496 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.00415 AC: 20 AN: 4816

European-Finnish (FIN) AF: 0.0755 AC: 797 AN: 10558

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

European-Non Finnish (NFE) AF: 0.0573 AC: 3897 AN: 67996

Other (OTH) AF: 0.0501 AC: 106 AN: 2114

Alfa AF: 0.0468 Hom.: 58

Bravo AF: 0.0458

Asia WGS AF: 0.00866 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.68
DANN	Benign	0.31
PhyloP100		-0.74
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: rs802024; hg19: chr7-86985719;