chr7-87357316-C-T

Position:

• chr7-87357316-C-T

Variant summary

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

The NM_021151.4(CROT):​c.116-1890C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0553 in 152,136 control chromosomes in the GnomAD database, including 303 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 0.055 (303 hom., cov: 31)
• Consequence: CROT NM_021151.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CROT	NM_021151.4	c.116-1890C>T		intron_variant		ENST00000331536.8	NP_066974.2
CROT	NM_001143935.2	c.116-191C>T		intron_variant			NP_001137407.1
CROT	NM_001243745.3	c.116-1890C>T		intron_variant			NP_001230674.1
CROT	XM_011516337.4	c.116-1890C>T		intron_variant			XP_011514639.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CROT	ENST00000331536.8	c.116-1890C>T		intron_variant		1	NM_021151.4	ENSP00000331981.4
CROT	ENST00000412227.6	c.116-1890C>T		intron_variant		1		ENSP00000404867.2
CROT	ENST00000419147.6	c.116-191C>T		intron_variant		2		ENSP00000413575.2
CROT	ENST00000442291.1	c.116-1890C>T		intron_variant		5		ENSP00000411983.1

Frequencies

GnomAD3 genomes AF: 0.0553 AC: 8407 AN: 152018 Hom.: 301 Cov.: 31

Gnomad AFR AF: 0.0682

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.0488

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.00435

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0573

Gnomad OTH AF: 0.0552

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

GnomAD4 genome AF: 0.0553 AC: 8420 AN: 152136 Hom.: 303 Cov.: 31 AF XY: 0.0548 AC XY: 4073 AN XY: 74386

Gnomad4 AFR AF: 0.0684

Gnomad4 AMR AF: 0.0338

Gnomad4 ASJ AF: 0.0488

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.00414

Gnomad4 FIN AF: 0.0753

Gnomad4 NFE AF: 0.0573

Gnomad4 OTH AF: 0.0546

Alfa AF: 0.0155 Hom.: 8

Bravo AF: 0.0532

Asia WGS AF: 0.00953 AC: 33 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.35

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: rs802025; hg19: chr7-86986632;